# Problem with CHARMM virtual sites in drug molecules **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdrun\ **Created:** [April 10, 2022, 5:10pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992 "2022-04-10T17:10:41Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![cdlorenz](https://avatars.discourse-cdn.com/v4/letter/c/9d8465/32.png) [@cdlorenz](https://gromacs.bioexcel.eu/u/cdlorenz)\ **Post date:** [April 10, 2022, 5:10pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/1 "2022-04-10T17:10:41Z")
GROMACS version: 2019 GROMACS modification: No I have used the Ligand Reader & Modeler on CHARMM-GUI to parameterise several different small molecules for simulation with lipid membranes. Those that have halogens with lone pairs modeled as virtual sites seem to lead to problems with running the simulations as I get " Fatal error: There is no domain decomposition for xx ranks that is compatible with the given box and a minimum cell size of y.yyyy nm" type errors. When I look in the log file it seems that one of the lone pair virtual sites is generally involved in the long distance interaction which results in the minimum cell size. I was wondering if anyone might have any suggestions as to how to get these models with virtual sites to work such that they can be run in parallel or is this just a ‘feature’ of these models with virtual sites? Thanks in advance- Chris ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [April 11, 2022, 2:06am UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/2 "2022-04-11T02:06:43Z")
What kind of virtual sites are you using? Can you please provide a specific example, which actual `.log` file output rather than having the values stripped out? Even better would be to upload a problematic ligand topology and corresponding `.log` file. ---
**Author:** ![cdlorenz](https://avatars.discourse-cdn.com/v4/letter/c/9d8465/32.png) [@cdlorenz](https://gromacs.bioexcel.eu/u/cdlorenz)\ **Post date:** [April 11, 2022, 5:36am UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/3 "2022-04-11T05:36:22Z")
Hi Prof Lemkul- I am unable to attach files since I am a new user of the forum it seems, so I will just copy and paste the log and itp files below so you can see them (sorry for such a clunky way to share the information). The virtual sites are of the type labeled as 3fad in the gromacs documentation I believe. (Note: I have removed some of the header lines of the log file and the position restrain lines of the itp to fit the restrictions on line numbers of posts.) Cheers- Chris * * * .log file :-) GROMACS - gmx mdrun, 2019.3 (-: . GROMACS: gmx mdrun, version 2019.3 Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018 Working dir: /lustre/scratch/mmm0050/biocides/bc\_176\_6 Process ID: 14584 Command line: gmx mdrun -v -deffnm step5\_1 GROMACS version: 2019.3 Precision: single Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) GPU support: disabled SIMD instructions: AVX\_512 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /shared/ucl/apps/intel/2018.Update3/compilers\_and\_libraries\_2018.3.222/linux/bin/intel64/icc Intel 18.0.3.20180410 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits C++ compiler: /shared/ucl/apps/intel/2018.Update3/compilers\_and\_libraries\_2018.3.222/linux/bin/intel64/icpc Intel 18.0.3.20180410 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits Running on 1 node with total 40 cores, 40 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz Family: 6 Model: 85 Stepping: 7 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Number of AVX-512 FMA units: 2 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Socket 1: [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 (2013) pp. 845-54 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- — Thank You — -------- -------- ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ > **[GROMACS 2019.3 Source code](https://zenodo.org/record/3243833)** > > Source code archive of the 2019.3 version of GROMACS. -------- -------- — Thank You — -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.001 nsteps = 125000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -1453863648 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 5000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.2 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 42 fourier-ny = 42 fourier-nz = 42 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = Nose-Hoover nsttcouple = 20 nh-chain-length = 1 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 grpopts: nrdf: 173 23211 ref-t: 303.15 303.15 tau-t: 1 1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Changing nstlist from 20 to 100, rlist from 1.2 to 1.298 Initializing Domain Decomposition on 40 ranks Dynamic load balancing: locked Minimum cell size due to atom displacement: 0.446 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 2.308 nm, Exclusion, atoms 1 70 multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 10 12 Minimum cell size due to bonded interactions: 2.538 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm Estimated maximum distance required for P-LINCS: 0.222 nm Guess for relative PME load: 0.20 Will use 32 particle-particle and 8 PME only ranks This is a guess, check the performance at the end of the log file Using 8 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 32 cells with a minimum initial size of 3.173 nm The maximum allowed number of cells is: X 1 Y 1 Z 1 * * * Program: gmx mdrun, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 0 (out of 40) Fatal error: There is no domain decomposition for 32 ranks that is compatible with the given box and a minimum cell size of 3.1731 nm Change the number of ranks or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at [Errors - Gromacs](http://www.gromacs.org/Documentation/Errors) * * * * * * .itp file ;; ;; Correspondance: ;; jul316@lehigh.edu or wonpil@lehigh.edu ;; ;; GROMACS topology file for LIG ;; [moleculetype] ; name nrexcl LIG 3 [atoms] ; nr type resnr residu atom cgnr charge mass 1 NG2D1 1 LIG N1 1 -0.952000 14.0070 ; qtot -0.952 2 CG2N1 1 LIG C1 2 0.669000 12.0110 ; qtot -0.283 3 NG311 1 LIG N2 3 -0.462000 14.0070 ; qtot -0.745 4 CG2N1 1 LIG C2 4 0.692000 12.0110 ; qtot -0.053 5 NG311 1 LIG N3 5 -0.392000 14.0070 ; qtot -0.445 6 CG2R61 1 LIG C3 6 -0.042000 12.0110 ; qtot -0.487 7 CG2R61 1 LIG C4 7 -0.118000 12.0110 ; qtot -0.605 8 CG2R61 1 LIG C5 8 -0.025000 12.0110 ; qtot -0.630 9 CG2R61 1 LIG C6 9 -0.101000 12.0110 ; qtot -0.731 10 BRGR1 1 LIG BR1 10 -0.170000 79.9040 ; qtot -0.901 11 CG2R61 1 LIG C7 11 0.411000 12.0110 ; qtot -0.490 12 CG2R61 1 LIG C8 12 -0.224000 12.0110 ; qtot -0.714 13 NG2D1 1 LIG N4 13 -0.944000 14.0070 ; qtot -1.658 14 NG311 1 LIG N5 14 -0.499000 14.0070 ; qtot -2.157 15 CG321 1 LIG C9 15 -0.057000 12.0110 ; qtot -2.214 16 CG321 1 LIG C10 16 -0.198000 12.0110 ; qtot -2.412 17 CG321 1 LIG C11 17 -0.180000 12.0110 ; qtot -2.592 18 CG321 1 LIG C12 18 -0.180000 12.0110 ; qtot -2.772 19 CG321 1 LIG C13 19 -0.198000 12.0110 ; qtot -2.970 20 CG321 1 LIG C14 20 -0.057000 12.0110 ; qtot -3.027 21 NG311 1 LIG N6 21 -0.499000 14.0070 ; qtot -3.526 22 CG2N1 1 LIG C15 22 0.669000 12.0110 ; qtot -2.857 23 NG311 1 LIG N7 23 -0.462000 14.0070 ; qtot -3.319 24 CG2N1 1 LIG C16 24 0.692000 12.0110 ; qtot -2.627 25 NG311 1 LIG N8 25 -0.392000 14.0070 ; qtot -3.019 26 CG2R61 1 LIG C17 26 -0.042000 12.0110 ; qtot -3.061 27 CG2R61 1 LIG C18 27 -0.118000 12.0110 ; qtot -3.179 28 CG2R61 1 LIG C19 28 -0.025000 12.0110 ; qtot -3.204 29 CG2R61 1 LIG C20 29 -0.101000 12.0110 ; qtot -3.305 30 BRGR1 1 LIG BR2 30 -0.170000 79.9040 ; qtot -3.475 31 CG2R61 1 LIG C21 31 0.411000 12.0110 ; qtot -3.064 32 CG2R61 1 LIG C22 32 -0.224000 12.0110 ; qtot -3.288 33 NG2D1 1 LIG N9 33 -0.944000 14.0070 ; qtot -4.232 34 NG2D1 1 LIG N10 34 -0.952000 14.0070 ; qtot -5.184 35 NG2O1 1 LIG N11 35 0.371000 14.0070 ; qtot -4.813 36 NG2O1 1 LIG N12 36 0.371000 14.0070 ; qtot -4.442 37 HGP1 1 LIG H1 37 0.370000 1.0080 ; qtot -4.072 38 HGPAM1 1 LIG H2 38 0.358000 1.0080 ; qtot -3.714 39 HGPAM1 1 LIG H3 39 0.369000 1.0080 ; qtot -3.345 40 HGR61 1 LIG H4 40 0.115000 1.0080 ; qtot -3.230 41 HGR62 1 LIG H5 41 0.146000 1.0080 ; qtot -3.084 42 HGR61 1 LIG H6 42 0.166000 1.0080 ; qtot -2.918 43 HGP1 1 LIG H7 43 0.370000 1.0080 ; qtot -2.548 44 HGPAM1 1 LIG H8 44 0.359000 1.0080 ; qtot -2.189 45 HGA2 1 LIG H9 45 0.090000 1.0080 ; qtot -2.099 46 HGA2 1 LIG H10 46 0.090000 1.0080 ; qtot -2.009 47 HGA2 1 LIG H11 47 0.090000 1.0080 ; qtot -1.919 48 HGA2 1 LIG H12 48 0.090000 1.0080 ; qtot -1.829 49 HGA2 1 LIG H13 49 0.090000 1.0080 ; qtot -1.739 50 HGA2 1 LIG H14 50 0.090000 1.0080 ; qtot -1.649 51 HGA2 1 LIG H15 51 0.090000 1.0080 ; qtot -1.559 52 HGA2 1 LIG H16 52 0.090000 1.0080 ; qtot -1.469 53 HGA2 1 LIG H17 53 0.090000 1.0080 ; qtot -1.379 54 HGA2 1 LIG H18 54 0.090000 1.0080 ; qtot -1.289 55 HGA2 1 LIG H19 55 0.090000 1.0080 ; qtot -1.199 56 HGA2 1 LIG H20 56 0.090000 1.0080 ; qtot -1.109 57 HGPAM1 1 LIG H21 57 0.359000 1.0080 ; qtot -0.750 58 HGPAM1 1 LIG H22 58 0.358000 1.0080 ; qtot -0.392 59 HGPAM1 1 LIG H23 59 0.369000 1.0080 ; qtot -0.023 60 HGR61 1 LIG H24 60 0.115000 1.0080 ; qtot 0.092 61 HGR62 1 LIG H25 61 0.146000 1.0080 ; qtot 0.238 62 HGR61 1 LIG H26 62 0.166000 1.0080 ; qtot 0.404 63 HGP1 1 LIG H27 63 0.370000 1.0080 ; qtot 0.774 64 HGP1 1 LIG H28 64 0.370000 1.0080 ; qtot 1.144 65 OG2N1 1 LIG O1 65 -0.311000 15.9994 ; qtot 0.833 66 OG2N1 1 LIG O2 66 -0.311000 15.9994 ; qtot 0.522 67 OG2N1 1 LIG O3 67 -0.311000 15.9994 ; qtot 0.211 68 OG2N1 1 LIG O4 68 -0.311000 15.9994 ; qtot -0.100 69 LPH 1 LIG LP1 69 0.050000 0.0000 ; qtot -0.050 70 LPH 1 LIG LP2 70 0.050000 0.0000 ; qtot 0.000 [bonds] ; ai aj funct b0 Kb 1 2 1 1 37 1 2 3 1 2 14 1 3 4 1 3 38 1 4 5 1 4 13 1 5 6 1 5 39 1 6 7 1 6 12 1 7 8 1 7 40 1 8 9 1 8 41 1 9 10 1 9 11 1 11 12 1 11 36 1 12 42 1 13 43 1 14 15 1 14 44 1 15 16 1 15 45 1 15 46 1 16 17 1 16 47 1 16 48 1 17 18 1 17 49 1 17 50 1 18 19 1 18 51 1 18 52 1 19 20 1 19 53 1 19 54 1 20 21 1 20 55 1 20 56 1 21 22 1 21 57 1 22 23 1 22 34 1 23 24 1 23 58 1 24 25 1 24 33 1 25 26 1 25 59 1 26 27 1 26 32 1 27 28 1 27 60 1 28 29 1 28 61 1 29 30 1 29 31 1 31 32 1 31 35 1 32 62 1 33 63 1 34 64 1 35 65 1 35 66 1 36 67 1 36 68 1 [pairs] ; ai aj funct c6 c12 or ; ai aj funct fudgeQQ q1 q2 c6 c12 1 4 1 1 15 1 1 38 1 1 44 1 2 5 1 2 13 1 2 16 1 2 45 1 2 46 1 3 6 1 3 15 1 3 37 1 3 39 1 3 43 1 3 44 1 4 7 1 4 12 1 4 14 1 5 8 1 5 11 1 5 38 1 5 40 1 5 42 1 5 43 1 6 9 1 6 13 1 6 36 1 6 41 1 7 10 1 7 11 1 7 39 1 7 42 1 7 69 1 8 12 1 8 36 1 9 40 1 9 42 1 9 67 1 9 68 1 10 12 1 10 36 1 10 41 1 11 41 1 12 39 1 12 40 1 12 67 1 12 68 1 12 69 1 13 38 1 13 39 1 14 17 1 14 37 1 14 38 1 14 47 1 14 48 1 15 18 1 15 49 1 15 50 1 16 19 1 16 44 1 16 51 1 16 52 1 17 20 1 17 45 1 17 46 1 17 53 1 17 54 1 18 21 1 18 47 1 18 48 1 18 55 1 18 56 1 19 22 1 19 49 1 19 50 1 19 57 1 20 23 1 20 34 1 20 51 1 20 52 1 21 24 1 21 53 1 21 54 1 21 58 1 21 64 1 22 25 1 22 33 1 22 55 1 22 56 1 23 26 1 23 57 1 23 59 1 23 63 1 23 64 1 24 27 1 24 32 1 24 34 1 25 28 1 25 31 1 25 58 1 25 60 1 25 62 1 25 63 1 26 29 1 26 33 1 26 35 1 26 61 1 27 30 1 27 31 1 27 59 1 27 62 1 27 70 1 28 32 1 28 35 1 29 60 1 29 62 1 29 65 1 29 66 1 30 32 1 30 35 1 30 61 1 31 61 1 32 59 1 32 60 1 32 65 1 32 66 1 32 70 1 33 58 1 33 59 1 34 57 1 34 58 1 35 62 1 35 70 1 36 42 1 36 69 1 40 41 1 41 69 1 44 45 1 44 46 1 45 47 1 45 48 1 46 47 1 46 48 1 47 49 1 47 50 1 48 49 1 48 50 1 49 51 1 49 52 1 50 51 1 50 52 1 51 53 1 51 54 1 52 53 1 52 54 1 53 55 1 53 56 1 54 55 1 54 56 1 55 57 1 56 57 1 60 61 1 61 70 1 [angles] ; ai aj ak funct th0 cth S0 Kub 2 1 37 5 1 2 3 5 1 2 14 5 3 2 14 5 2 3 4 5 2 3 38 5 4 3 38 5 3 4 5 5 3 4 13 5 5 4 13 5 4 5 6 5 4 5 39 5 6 5 39 5 5 6 7 5 5 6 12 5 7 6 12 5 6 7 8 5 6 7 40 5 8 7 40 5 7 8 9 5 7 8 41 5 9 8 41 5 8 9 10 5 8 9 11 5 10 9 11 5 9 11 12 5 9 11 36 5 12 11 36 5 6 12 11 5 6 12 42 5 11 12 42 5 4 13 43 5 2 14 15 5 2 14 44 5 15 14 44 5 14 15 16 5 14 15 45 5 14 15 46 5 16 15 45 5 16 15 46 5 45 15 46 5 15 16 17 5 15 16 47 5 15 16 48 5 17 16 47 5 17 16 48 5 47 16 48 5 16 17 18 5 16 17 49 5 16 17 50 5 18 17 49 5 18 17 50 5 49 17 50 5 17 18 19 5 17 18 51 5 17 18 52 5 19 18 51 5 19 18 52 5 51 18 52 5 18 19 20 5 18 19 53 5 18 19 54 5 20 19 53 5 20 19 54 5 53 19 54 5 19 20 21 5 19 20 55 5 19 20 56 5 21 20 55 5 21 20 56 5 55 20 56 5 20 21 22 5 20 21 57 5 22 21 57 5 21 22 23 5 21 22 34 5 23 22 34 5 22 23 24 5 22 23 58 5 24 23 58 5 23 24 25 5 23 24 33 5 25 24 33 5 24 25 26 5 24 25 59 5 26 25 59 5 25 26 27 5 25 26 32 5 27 26 32 5 26 27 28 5 26 27 60 5 28 27 60 5 27 28 29 5 27 28 61 5 29 28 61 5 28 29 30 5 28 29 31 5 30 29 31 5 29 31 32 5 29 31 35 5 32 31 35 5 26 32 31 5 26 32 62 5 31 32 62 5 24 33 63 5 22 34 64 5 31 35 65 5 31 35 66 5 65 35 66 5 11 36 67 5 11 36 68 5 67 36 68 5 [dihedrals] ; ai aj ak al funct phi0 cp mult 3 2 1 37 9 14 2 1 37 9 1 2 3 4 9 1 2 3 38 9 14 2 3 38 9 1 2 14 15 9 1 2 14 44 9 3 2 14 15 9 3 2 14 44 9 4 3 2 14 9 2 3 4 5 9 2 3 4 13 9 5 4 3 38 9 13 4 3 38 9 3 4 5 6 9 3 4 5 39 9 13 4 5 39 9 3 4 13 43 9 5 4 13 43 9 6 5 4 13 9 4 5 6 7 9 4 5 6 12 9 7 6 5 39 9 12 6 5 39 9 5 6 7 8 9 5 6 7 40 9 12 6 7 40 9 5 6 12 11 9 5 6 12 42 9 7 6 12 11 9 7 6 12 42 9 8 7 6 12 9 6 7 8 9 9 6 7 8 41 9 40 7 8 41 9 9 8 7 40 9 7 8 9 10 9 7 8 9 11 9 10 9 8 41 9 11 9 8 41 9 8 9 11 12 9 8 9 11 36 9 10 9 11 12 9 10 9 11 36 9 9 11 12 42 9 36 11 12 42 9 9 11 36 67 9 9 11 36 68 9 12 11 36 67 9 12 11 36 68 9 6 12 11 9 9 6 12 11 36 9 2 14 15 16 9 2 14 15 45 9 2 14 15 46 9 44 14 15 45 9 44 14 15 46 9 16 15 14 44 9 14 15 16 17 9 14 15 16 47 9 14 15 16 48 9 45 15 16 47 9 45 15 16 48 9 46 15 16 47 9 46 15 16 48 9 17 16 15 45 9 17 16 15 46 9 15 16 17 18 9 15 16 17 49 9 15 16 17 50 9 47 16 17 49 9 47 16 17 50 9 48 16 17 49 9 48 16 17 50 9 18 17 16 47 9 18 17 16 48 9 16 17 18 19 9 16 17 18 51 9 16 17 18 52 9 49 17 18 51 9 49 17 18 52 9 50 17 18 51 9 50 17 18 52 9 19 18 17 49 9 19 18 17 50 9 17 18 19 20 9 17 18 19 53 9 17 18 19 54 9 51 18 19 53 9 51 18 19 54 9 52 18 19 53 9 52 18 19 54 9 20 19 18 51 9 20 19 18 52 9 18 19 20 21 9 18 19 20 55 9 18 19 20 56 9 53 19 20 55 9 53 19 20 56 9 54 19 20 55 9 54 19 20 56 9 21 20 19 53 9 21 20 19 54 9 19 20 21 22 9 19 20 21 57 9 55 20 21 57 9 56 20 21 57 9 22 21 20 55 9 22 21 20 56 9 20 21 22 23 9 20 21 22 34 9 23 22 21 57 9 34 22 21 57 9 21 22 23 24 9 21 22 23 58 9 34 22 23 58 9 21 22 34 64 9 23 22 34 64 9 24 23 22 34 9 22 23 24 25 9 22 23 24 33 9 25 24 23 58 9 33 24 23 58 9 23 24 25 26 9 23 24 25 59 9 33 24 25 59 9 23 24 33 63 9 25 24 33 63 9 26 25 24 33 9 24 25 26 27 9 24 25 26 32 9 27 26 25 59 9 32 26 25 59 9 25 26 27 28 9 25 26 27 60 9 32 26 27 60 9 25 26 32 31 9 25 26 32 62 9 27 26 32 31 9 27 26 32 62 9 28 27 26 32 9 26 27 28 29 9 26 27 28 61 9 60 27 28 61 9 29 28 27 60 9 27 28 29 30 9 27 28 29 31 9 30 29 28 61 9 31 29 28 61 9 28 29 31 32 9 28 29 31 35 9 30 29 31 32 9 30 29 31 35 9 29 31 32 62 9 35 31 32 62 9 29 31 35 65 9 29 31 35 66 9 32 31 35 65 9 32 31 35 66 9 26 32 31 29 9 26 32 31 35 9 [dihedrals] ; ai aj ak al funct q0 cq 2 14 3 1 2 4 3 5 13 2 22 21 23 34 2 24 23 25 33 2 [virtual\_sites3] ; Site from funct theta d 69 10 9 8 3 180.00 0.189 70 30 29 28 3 180.00 0.189 [exclusions] ; ai aj 69 10 1 69 9 1 69 8 1 69 7 1 69 41 1 69 11 1 69 12 1 69 36 1 70 30 1 70 29 1 70 28 1 70 27 1 70 61 1 70 31 1 70 32 1 70 35 1 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [April 13, 2022, 2:35am UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/4 "2022-04-13T02:35:59Z")
The exclusions are the limiting factor here, and the only solution is to use fewer processors such that the DD cell sizes are larger and therefore compatible with the topology’s requirements. ---
**Author:** ![cdlorenz](https://avatars.discourse-cdn.com/v4/letter/c/9d8465/32.png) [@cdlorenz](https://gromacs.bioexcel.eu/u/cdlorenz)\ **Post date:** [April 13, 2022, 5:05am UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/5 "2022-04-13T05:05:07Z")
Ok, thanks a lot. Cheers- Chris ---
**Author:** ![Saimaejaz](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@Saimaejaz](https://gromacs.bioexcel.eu/u/Saimaejaz)\ **Post date:** [December 5, 2022, 4:47am UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/6 "2022-12-05T04:47:09Z")
hello, I have a query… i thought you can help me out because i read your posts. Actually I am running 50ns md simulation on GROMACS. I have used CHARMM-GUI for initial file preparation… After that i used following commands for md run gmx grompp -f mdout.mdp -c step4.1\_equilibration.gro -t step4.1\_equilibration.cpt -p topol.top -n index.ndx -o md\_0\_50.tpr gmx mdrun -v -deffnm md\_0\_50 In RUN CONTROL PARAMETERS dt= 0.001 nsteps= 125000 why this is so??? because we have studied in MD Simulation during my course of MD Simulation that for 1ns = 1000ps = 500000 nsteps but here when i run the simulation of 50ns why nsteps are showing as 125000 125.0ps on my console?? why calculation is different. Is there any error in my command? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 5, 2022, 7:57pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/7 "2022-12-05T19:57:15Z")
CHARMM-GUI has a very specific set of equilibration steps for gradually removing restraints. It does 125 ps at a given force constant, then releases that and applies a different one, etc. Refer to the CHARMM-GUI papers if this is unfamiliar to you. ---
**Author:** ![Saimaejaz](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@Saimaejaz](https://gromacs.bioexcel.eu/u/Saimaejaz)\ **Post date:** [December 6, 2022, 1:42pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/8 "2022-12-06T13:42:42Z")
thanks alot Regards. ---
**Author:** ![Saimaejaz](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@Saimaejaz](https://gromacs.bioexcel.eu/u/Saimaejaz)\ **Post date:** [December 17, 2022, 6:01pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/9 "2022-12-17T18:01:51Z")
Hello, I Hope you are doing well. I have two queries. I want to extract the trajectory of my 50ns simulation (protein-protein) below is the input command. gmx trjconv -s md\_0\_50.tpr -f md\_0\_50.xtc -o traj.pdb -dt 1. Actually, I am a beginner, and I want to know how to get a trajectory of full 50ns (not a specific frame.) the -dt 1 means what?? 2nd Question After extending my simulation to 100ns. After completion I only get three files: .tpr , .cpt and mdp.out. I didn’t get the xtc file?? Is it ok?? And I want to extract the trajectory with this input command as I have no .xtc file generated after extension. Will this .cpt work? gmx trjconv -s md\_0\_100.tpr -f md\_0\_100.cpt -o traj.pdb -dt 1 I hope to hear from you soon. Regards Saima Ejaz ---
**Author:** ![Saimaejaz](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@Saimaejaz](https://gromacs.bioexcel.eu/u/Saimaejaz)\ **Post date:** [December 17, 2022, 6:20pm UTC](https://gromacs.bioexcel.eu/t/problem-with-charmm-virtual-sites-in-drug-molecules/3992/10 "2022-12-17T18:20:19Z")
hello, i want to add one thing more in my 2nd question, .part0002.xtc file is generated after extension of md simulation from 50ns to 100ns. Regards, Saima Ejaz