[gmx-users] Using CPU with GPU

=$PBS_O_WORKDIR export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` export DIR=/work/rj/work_file  cd $DIR mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -nb gpu -de

[gmx-users] Running ultiple job in core?

Hi there, I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two simulation job by assigning 12 threads for each job. I have tried using "-ntomp 12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt get the similar speed as if run them alone with 12 threads. I

[gmx-users] H-bond calculation

Dear gmx, I would like to calculate the H-bond occupancy between two residue (intra mol inter Thr183 (OG1) -Tyr162 (N) ). I made a .ndx file choosing the both atoms : Group40 ( r_162_&_N) has 1 elements Group

[gmx-users] probability distributions in gmx

Dear gmx, I understand that probability distributions of distance can be calculated through gmx analyze tool but how the probability distributions of others such as SASA and secondary structure can be calculated? Do i have to use other plotting tool R, gnuplot to do ? or can any gromacs tool

[gmx-users] gmx cluster cut off

Dear all, I have done protein with three different inhibitor for 100ns simulation and would use the most populated structure for further analysis. What i wonder is how do i select the perfect cut off value to choose the most populated structure from 100ns? Is that following command can prov

[gmx-users] Best step to run simulation over GPU?

Dear gmx, I have a single PC contains 24 threads with GTX 980Ti. I would like to know how do i run the 3 or 2 simulation in same time with above mentioned PC would have similar speed. I also read about -pin options but couldnt understand well. Moreover i run in default i get this error "The G

[gmx-users] Re; .xtc and .trr file is missing

ble to get those file using the .cpt file? Any suggestion would be appreciated. Thanks. To: Discussion list for GROMACS users Subject: Re: [gmx-users] .xtc and .trr file is missing Message-ID: Content-Type: text/plain; charset=UTF-8 Hi RJ, For an XTC file, you need to set nstxtcout (G

[gmx-users] .xtc and .trr file is missing

Dear gmx. I run 100ns simulation of my protein with ligand. After completing the 100ns, the output doesnt give .xtc and .tpr files of final output. i could find .cpt .edr .gro .tpr files of final output. Please guide me how can i get the final output of these files ? Thanks -- Gromacs Users

Re: [gmx-users] Running Multiple simulation in single PC

Thanks Carsten. I already compiled with openmpi and it works fine. I also found that -ntomp and -ntmpi functions and used them, > On 30 Apr 2015, at 04:14, ? wrote: > > Dear Carsten, > > > Thank you for suggestion. > > > Should i need to compile with OpenMP even if i dont use clu

[gmx-users] Running Multiple simulation in single PC.

Dear all, I have a 64 bit PC with 16 processor with GTX460 gpu and wants to run multiple simulation. One simulation takes (~120 aa length) for 100ns about 4-5 days, whereas when i subject same protein into 100ns, it shows it will take over a month to finish. Is that any command that can us

[gmx-users] Using gmx 5.0.4 made traj to analyze in gromac 4.6 version

Dear gmx users, I used gmx 5.0.4 for MD runs, and for the purpose of MMPBSA analysis ( only compatible with 4.6 version) i used those files in gromacs 4.6 but end up with errors: By looking at the previous similar issues mail, i tried to make .tpr in gromacs 4.6 version but i couldnt able to

[gmx-users] DSSP with gmx 5.0.4

Dear gmx users, I tried DSSP of both binary and .exe by renaming it as dssp (dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in usr/local/bin/dssp. set the excusable too ( "which dssp" /usr/local/bin/dssp). Both of them gives

[gmx-users] Gromacs running on single PC with GPU?

Dear gmx I have PC has 16 processor with GTX460 where i complied successfully by following the gmx procedure. When i run gmx mdrun, it does detects my gpu but i wonder whether its taking for calculation or not ? Here i get this info while running mdrun Using 1 MPI thread Using 16 OpenMP th

Re: [gmx-users] Environmental variable setting for gmx 5.0.4

. Any suggestion plz? Date: Wed, 1 Apr 2015 17:20:29 +0900 From: yoochan To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Environmental variable setting for gmx 5.0.4 Message-ID: <53f2341b-5a16-48df-a520-5d0c26afd...@gmail.com> Content-Type: text/plain; charset=utf-8 Hi RJ, I

[gmx-users] Environmental variable setting for gmx 5.0.4

Dear gmx, I have installed the gmx in my ubuntu and centos system and tried to set the environmental variable path in-order to use without mentioning the source commend in my terminal of linux. I tried to set my path as follows but couldn't success it. export PATH=/usr/local/gromacs/bin/:$PAT

[gmx-users] pdb2gmx error

Dear gmx, I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even cleaned my crystal structure using Discovery studio/swissviewer which shows no error on it. I wonder, how do i rectify this problem ? WARNING: WARNING: Residue 1 named MET of a molecule in the input file was m

[gmx-users] potential energy is from energy mimization

Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 1162 steps Potent

[gmx-users] free energy perturbation methods in gmx

-activation caused my Mutant in protein? Much appreciated for your valuable suggestion. Regards RJ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Su

[gmx-users] make_ndx specific residues backbone in Chain A and B

Dear all, How do i select different chain backbone in make_ndx ? i could select the chain A and B desperately but cant select them together. The manual says 'chain' ch1 [ch2 ..] I tried as like the manual, but end up with error; chain A | chain B & r 236-297 | r 321-400 | r 433-512 | r 52

[gmx-users] Re;calculating interaction energies of dimers and ligand

open file: topol.tpr Dear Justin, I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies? what does mdrun -rerun ? On 2/13/15 7:07 AM, RJ wrote: > Dear all, > >

[gmx-users] calculating interaction energies of dimers and ligand

n to indicate the group of residues so? Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)? Thanks Regards RJ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Calculating the interaction energy as well individual energy?

Hello, Whats the way to calculate the individual residue energy (eg: His would have different energy upon different protonation)? How do we also calculate the interaction energy of ligand molecules with particular residues? -- Gromacs Users mailing list * Please search the archive at h

[gmx-users] Charges & non-bonded interaction values usage in different force fields

Dear all, Experimentally determined charges and non-bonded interaction values for ligand atoms ( Written in charmm) can be used directly in gromacs provided charmm27.ff ? or does it need any conversion to use it in gromacs based charmm27.ff? -- Gromacs Users mailing list * Please search t