# Using GPU to run NVT, NPT and MD run **URL:** \ **Category:** User discussions\ **Created:** [September 9, 2021, 11:45am UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790 "2021-09-09T11:45:38Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![farial.t](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@farial.t](https://gromacs.bioexcel.eu/u/farial.t)\ **Post date:** [September 9, 2021, 11:45am UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/1 "2021-09-09T11:45:38Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I need to run md simulation on my protein with an unnatural residue (formyl glycine). so I had to download charmm27.ff from [SwissSidechain - A database of non-natural sidechains](https://www.swisssidechain.ch/MD/gromacs.php) server to create the required topology. Then used 2 versions of GROMACS. the first one is gromacs-2016.4 applied to make topology, solavation and energy minimization . the second one is applied to run NVT/NPT and MD on GPU. but when issued this command gmx mdrun -deffnm md\_0\_1 -nb gpu to run NVT on GPU , faced this error: can not run short-ranged nonbonded interactions on a GPU because there is no detected. the NVT.mdp file which I used is: title = CHARMM27 ARSA NVT equilibration define = -DUSE\_OLD\_C36m ; Run parameters integrator = md ; leap-frog integrator nsteps = 200000 ; 2 \* 200000 = 400 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw-switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau\_t = 0.1 0.1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 300 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed I would be really grateful if anyone can help me to understand and solve it out. sincerly Farial ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [September 10, 2021, 12:22pm UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/2 "2021-09-10T12:22:11Z")
Hi, you wrote that you use two GROMACS version, one is 2016.4 and which is the other one? \Alessandra ---
**Author:** ![farial.t](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@farial.t](https://gromacs.bioexcel.eu/u/farial.t)\ **Post date:** [September 11, 2021, 8:21am UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/3 "2021-09-11T08:21:45Z")
Dear Alevia Sorry for making mistake the second one is GROMACS 2018.0 sincerely Farial ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [September 13, 2021, 8:40am UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/4 "2021-09-13T08:40:59Z")
Hi, Have you generate the tpr file for NVT/NPT simulations using version 2018? What exactly says the error you got? Best regards Alessandra ---
**Author:** ![farial.t](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@farial.t](https://gromacs.bioexcel.eu/u/farial.t)\ **Post date:** [October 27, 2021, 12:07pm UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/5 "2021-10-27T12:07:52Z")
[faryal.tavakoli@gmail.com](mailto:faryal.tavakoli@gmail.com) attached a document ![Unknown profile photo](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/782af51dd4621f3200db709c68166895d095c8f6.png) [faryal.tavakoli@gmail.com](mailto:faryal.tavakoli@gmail.com) has attached the following document: This is an informative file including WTSGC.mol2. WTSGC.pdb and WTSGC.itp files. ![](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a39457cb094c59e9d31d77ee63b529367b2fa5af.png)informative file Google LLC, 1600 Amphitheatre Parkway, Mountain View, CA 94043, USA You have received this email because [faryal.tavakoli@gmail.com](mailto:faryal.tavakoli@gmail.com) shared a document with you from Google Docs. [![Logo for Google Docs](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/54a4d3513f6a9fb87a5b2da8d9247dda14d9a65d.png)](https://www.google.com/) (Attachment informative file.pdf is missing) ---
**Author:** ![farial.t](https://avatars.discourse-cdn.com/v4/letter/f/ccd318/32.png) [@farial.t](https://gromacs.bioexcel.eu/u/farial.t)\ **Post date:** [October 27, 2021, 12:22pm UTC](https://gromacs.bioexcel.eu/t/using-gpu-to-run-nvt-npt-and-md-run/2790/6 "2021-10-27T12:22:17Z")
[faryal.tavakoli@gmail.com](mailto:faryal.tavakoli@gmail.com) attached a document ![Unknown profile photo](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/782af51dd4621f3200db709c68166895d095c8f6.png) [faryal.tavakoli@gmail.com](mailto:faryal.tavakoli@gmail.com) has attached the following document: Dear Dr.Alevilla This is an informative file including WTSGC.mol2. WTSGC.pdb and WTSGC.itp file and this is my topology file ; ; File ‘topol.top’ was generated ; By user: vaio (1000) ; On host: vaio-VPCEA42EG ; At date: Sat Oct 16 21:39:04 2021 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2016.4 (-: ; ; Executable: /usr/local/gromacs/bin/gmx ; Data prefix: /usr/local/gromacs ; Working dir: /media/vaio/Apacer PHD/ARSA/docking results/SGC/WT ; Command line: ; gmx pdb2gmx -f ARSA.pdb -o ARSA.gro -ignh ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters #include “./charmm27.ff/forcefield.itp” ; Include chain topologies #include “WTSGC.itp” #include “topol\_pro\_chain\_A.itp” ; Include water topology #include “./charmm27.ff/tip3p.itp” #ifdef POSRES\_WATER ; Position restraint for each water oxygen [position\_restraints] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include “./charmm27.ff/ions.itp” [system] ; Name Protein in water [molecules] ; Compound #mols Protein\_chain\_A 1 WTSGC 1 SOL 18250 ![](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a39457cb094c59e9d31d77ee63b529367b2fa5af.png)informative file Snapshot of the item below: WTSGC.mol2