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
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.
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 ++++
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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
.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
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.
Ok, thanks a lot.
Cheers-
Chris
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?
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.
thanks alot
Regards.
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
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