[gmx-users] Separate removal of COM motion

2018-01-16 Thread R
Dear all I am involved in a project where the target systems are lipid bilayers with and without different macromolecules embedded. In the past I did quite a lot of MD simulations of membrane systems always removing the COM motion of lipids and the solvent in separate groups. There are

[gmx-users] Long Simulations in Batch GMX 2018

2018-03-13 Thread R
Dear all, I am doing a simulation of protein of my interest. I could run the simulation following the lysozyme tutorial. I am using 2018 version for gromacs. To start with, I ran the simulation for 1 ns. I want to run long simulation though want to make sure that each trajectory files has a

[gmx-users] Managing long simulations GMX 2018

2018-03-15 Thread R
rences between state.cpt and state_prev.cpt? I am back to simulations after years, last I used was gromacs 3.x series. Things are bit different now ! Thanks a lot for your help. Best, R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] running parallel simulations on different of cores

2014-04-19 Thread Muthukumaran R
Dear gromacs users, I have been working on gromacs package for performing md simulations. recently i have started using cluster with 2 nodes with 64 cores each. I am eager to know whether a job run on 32 cores for few ns and later i continue the same job on 64 cores (or vice versa), will show any

[gmx-users] add NaCl

2015-08-18 Thread mohammad r
Hi; I've already converted topology and coordinate files which were generated with amber tools to .gro format. But now, when I want to add 100Mm NaCl to the system I get this error: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'c6m1_GMX.top' For more

[gmx-users] energy minimization

2015-08-19 Thread mohammad r
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

2015-08-19 Thread mohammad r
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

2015-08-19 Thread mohammad r
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

2015-08-19 Thread mohammad r
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] atom types IP and IM

2015-08-20 Thread mohammad r
Hi; I've used ff14sbamber force field to generate my system. As this force field doesn'texist in gromacs, I generated the first structure of my system withamber tools then I converted the topology and coordinate files intogromacs format by using acpype. (In the amber tools I've added NaClto my

[gmx-users] acpype problem

2015-08-18 Thread mohammad r
Hi; I want to convert amber topology and coordinate files into gromacs topology and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not found I've done the procedure mentioned in the website:

[gmx-users] force field

2015-08-09 Thread mohammad r
Hi; I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add it in?Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] force field

2015-08-09 Thread mohammad r
of the present forcefields in gromacs. Regards,-Maryam On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote: Hi; I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add

[gmx-users] adding lipids

2015-09-10 Thread mohammad r
Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I

[gmx-users] adding lipids

2015-09-10 Thread mohammad r
Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I

[gmx-users] installing GROMACS

2015-10-04 Thread mohammad r
Hi; I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the gromacs.org, but I got an error after typing "cmake .. " line, then I tried "sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I want the gromacs-5.0.5. what should I do? Thank you,

[gmx-users] installing gromacs-5.0.5

2015-10-05 Thread mohammad r
Hello everybody; I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation instruction in the website "gromacs.org", but in the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error: -- No compatible CUDA toolkit found (v4.0+), disabling native GPU

[gmx-users] Equilibration fails only when run from script

2015-12-01 Thread R Corey
Hello I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a steepest descents minimization, NVT equil, NPT equil and production run, all controlled by a central script. However, only about 50% of the runs get through the NVT equilibration without crashing - crash error as

[gmx-users] convert amber files to gromacs

2015-11-24 Thread mohammad r
Hi everybody,   I want to convert the topology and coordinate files fromamber to gromacs format. I used acpype bu it didn’t work properly (actually mysystem is consisted of some lipids in a water-protein system but when I convertthe files via acpype, the backbone is consisted of a mass

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-16 Thread Husen R
On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Thu, Jun 16, 2016 at 9:30 AM Husen R <hus...@gmail.com> wrote: > > > Hi, > > > > Thank you for your reply ! > > > > md_test.xtc is exist and writa

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-16 Thread Husen R
in the check > that takes place when the checkpoint is read is not relevant to the > problem. > > Mark > > On Thu, Jun 16, 2016 at 9:46 AM Husen R <hus...@gmail.com> wrote: > > > On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham <mark.j.abra...@gmail.com> >

Re: [gmx-users] How does gromacs checkpoint works

2016-06-23 Thread Husen R
all your ranks/cores choosing to checkpoint at the same time. > Pick a portable file format. > > Mark > > On Thu, Jun 23, 2016 at 4:15 AM Husen R <hus...@gmail.com> wrote: > > > Hi all, > > > > For academic purpose, I'm wondering how does checkpoint feature in &

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-23 Thread Husen R
s per node:4 Logical cores per node:8 Hardware detected on host head-node (the node of MPI rank 0): CPU info: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz SIMD instructions most likely to fit this hardware: AVX_256 SIMD instructions selected

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-23 Thread Husen R
doing. > > Mark > > On Thu, Jun 23, 2016 at 10:15 AM Husen R <hus...@gmail.com> wrote: > > > Hi, > > > > I still unable to find out the cause of the fatal error. > > Previously, gromacs is installed in every nodes. That's the cause Build > > time m

Re: [gmx-users] How does gromacs checkpoint works

2016-06-23 Thread Husen R
Hi Mark, Thank you very much! Regards, Husen On Thu, Jun 23, 2016 at 3:42 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Yes > > On Thu, Jun 23, 2016 at 9:54 AM Husen R <hus...@gmail.com> wrote: > > > Hi, > > > > Could you tell me the locat

[gmx-users] How does gromacs checkpoint works

2016-06-22 Thread Husen R
Hi all, For academic purpose, I'm wondering how does checkpoint feature in Gromacs works ? is there any resource/tutorial that I can learn ? Thank you in advance, Husen -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-15 Thread Husen R
Hi all, I got the following error message when I tried to restart gromacs simulation from checkpoint file. I restart the simulation using fewer nodes and processes, and also I exclude one node using '--exclude=' option (in slurm) for experimental purpose. I'm sure fewer nodes and processes are

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-15 Thread Husen R
PROCESSES = PID 6983 RUNNING AT head-node = EXIT CODE: 1 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES === On Thu, Jun 16, 2016 at 11:48 AM, Husen R <hus...@gmail.com>

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

2016-06-16 Thread Husen R
t tried to operate > upon md_test.xtc, so perhaps you need to consider whether the file exists, > is writable, etc. > > Mark > > On Thu, Jun 16, 2016 at 6:48 AM Husen R <hus...@gmail.com> wrote: > > > Hi all, > > > > I got the following error message when

[gmx-users] DMF molecule

2016-02-08 Thread mohammad r
Hi everybody, I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command, but the residues are not included in none of the forcefields. can you please help me figure this out? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] DSSP secondary structure

2016-02-12 Thread mohammad r
Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] modeling CNT, center of mass velocity, energy minimization

2016-02-23 Thread mohammad r
Hi GROMACS users,  I have some questions:  1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field?2-  How can I check the centerof mass velocity of my system?3-  I want to calculate volumeand water self diffusion coefficient

Re: [gmx-users] DSSP secondary structure

2016-02-14 Thread mohammad r
I changed and reduced the ratio but the xpm file was not changed at all. On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/14/16 1:54 AM, mohammad r wrote: > Thank you Justin, > > I used xpm2ps command with below m2p file but

Re: [gmx-users] DSSP secondary structure

2016-02-15 Thread mohammad r
, 2016 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/15/16 1:31 AM, mohammad r wrote: > I changed and reduced the ratio but the xpm file was not changed at all. > Unfortunately there's not much I can tell you here because this is rather cryptic.  It's illogical to get the

[gmx-users] converted topology from amber to gromacs

2016-02-18 Thread mohammad r
Hi gromacs users, I've generatedinitial structure of my system by using ambertools (topology andcoordinate files) and converted it to gromacs format (.gro and .top)by parmed, but in topology file it doesn't refer to any forcefield.Does it make any problem in the results or it is ok? Because

Re: [gmx-users] converted topology from amber to gromacs

2016-02-21 Thread mohammad r
Thank you very much Justin On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/20/16 8:49 AM, mohammad r wrote: > Hi Justin, > > Thank you for your answer, I used grompp and it didn't give me error. I've > attached a topology file

[gmx-users] Potential energy

2016-02-21 Thread mohammad r
Hi everybody,   Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html Thank you, Mohammad. -- Gromacs Users

Re: [gmx-users] Potential energy

2016-02-21 Thread mohammad r
Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/21/16 3:15 PM, mohammad r wrote: > Hi everybody, > > > > Is it correct to say the p

Re: [gmx-users] DSSP secondary structure

2016-02-13 Thread mohammad r
edu> wrote: On 2/13/16 1:33 AM, mohammad r wrote: > Hi, > I used the "gmx do_dssp" command to get the secondary structure of the > protein during the simulation but the resolution of the resulted .xpm file is > very low. how can I increase its resolution? You can a

[gmx-users] modeling CNT, center of mass velocity, energy minimization

2016-02-21 Thread mohammad r
Hi GROMACS users,   I have some questions:   1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field? 2-  How can I check the centerof mass velocity of my system? 3-  I want to calculate volumeand water self diffusion

Re: [gmx-users] Neutralizing

2016-03-09 Thread mohammad r
Thank you Justin for your help. On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/9/16 1:42 AM, mohammad r wrote: > Thank you Parham and Justin, Excuse me I have another question, in simulation > of a water-peptide system, is it necessary

Re: [gmx-users] Neutralizing

2016-03-08 Thread mohammad r
Lemkul <jalem...@vt.edu> wrote: On 3/8/16 3:59 AM, mohammad r wrote: > Thank you Parham > You mean that it is not necessary to do QM/MM simulation? > The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like

Re: [gmx-users] QM calculation

2016-03-30 Thread mohammad r
AM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/30/16 2:17 AM, mohammad r wrote: > Hi gromacs users, > > > > I want to do QMcalculation to my system. Can the PRODRG sitedo it (according > to gromacs tutorial)? Or I should do it by using gromacsitself? By

[gmx-users] Run mdrun in parallel

2016-04-12 Thread Husen R
Hi all, Currently, I'm trying to run mdrun command in parallel. the following is my batch script using Slurm as a resource manager: =Batch Script== #!/bin/bash #SBATCH -J Eq1 #SBATCH -o eq1-%j.out #SBATCH -A pro #SBATCH -N 2 #SBATCH -n 16 gmx mdrun -deffnm

Re: [gmx-users] Gromacs 5.1.2 installation problem

2016-04-05 Thread Husen R
ption to > use it the old way as well. > > Regards, > James > > > On 05/04/16 08:19, Husen R wrote: > >> Dear all, >> >> I already installed gromacs-5.1.2 succesfully with the following >> instruction : >> >> tar xfz gromacs-5.1.2.tar.gz >&g

Re: [gmx-users] Neutralizing

2016-03-08 Thread mohammad r
cation ::: Website ::: FaceBook On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote: Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/M

[gmx-users] Neutralizing

2016-03-07 Thread mohammad r
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Gromacs 5.1.2 installation problem

2016-04-05 Thread Husen R
Dear all, I already installed gromacs-5.1.2 succesfully with the following instruction : tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC However, after

Re: [gmx-users] QM calculation

2016-03-31 Thread mohammad r
Thank you very much Justin for your helpful answer. On Thursday, March 31, 2016 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/31/16 12:19 AM, mohammad r wrote: > Thank you Justin, I want to do QM calculationbefore running equilibration > then run the MD simulation by

[gmx-users] QM calculation

2016-03-30 Thread mohammad r
Hi gromacs users,   I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve generated the initial coordinate and topology files inamber tools then convert it to gromacs format by using parmed

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

2016-04-24 Thread Husen R
Hi, Thanks a lot ! I'll try it,.. Regards, Husen On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/24/16 12:04 AM, Husen R wrote: > >> Dear all, >> >> is there any complete documentation discussing checkpoint/restart in >

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

2016-04-26 Thread Husen R
: md_0_1.cpt and md_0_1_prev.cpt is this because of -deffnm option ? I just want to make sure. Regards, Husen On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, 26 Apr 2016 06:19 Husen R <hus...@gmail.com> wrote: > > >

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

2016-04-25 Thread Husen R
--mail-user=hus...@gmail.com #SBATCH --mail-type=begin #SBATCH --mail-type=end mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1 Thank you in advance Regards, Husen On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote: > Hi, > > Thanks a lot ! > I'll try

[gmx-users] Gromacs-5.1.2 Checkpoint/restart example

2016-04-23 Thread Husen R
Dear all, is there any complete documentation discussing checkpoint/restart in Gromacs-5.1.2 ? I found this link that discuss checkpoint ( http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and this link that discuss restart (

[gmx-users] Adding ions

2016-05-22 Thread mohammad r
Hi GROMACS users, I solved my proteinin a defined box of water. Now I want to add ions to neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro -pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror : Fatal error:No such moleculetypeSOLFor more informationand

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

2016-05-16 Thread Husen R
anual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects > >> > (These thoughts are common to earlier versions also.) > >> > > >> > Mark > >> > > >> > > >> > Best wishes > >> >> Jame

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

2016-05-13 Thread Husen R
I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager. On Sat, May 14, 2016 at 7:53 AM, Husen R <hus...@gmail.com> wrote: > Dear all > > Does simulation able to be restarted from checkpoint file with fewer nodes > ? > let's say, at the first time, I run simulation wit

[gmx-users] Restart simulation from checkpoint file with fewer nodes

2016-05-13 Thread Husen R
Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that simulation immadiately based on checkpoint

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

2016-05-13 Thread Husen R
Lemkul <jalem...@vt.edu> wrote: > > > On 5/13/16 8:53 PM, Husen R wrote: > >> Dear all >> >> Does simulation able to be restarted from checkpoint file with fewer >> nodes ? >> let's say, at the first time, I run simulation with 3 nodes. A

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

2016-05-14 Thread Husen R
, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/13/16 8:53 PM, Husen R wrote: > >> Dear all >> >> Does simulation able to be restarted from checkpoint file with fewer >> nodes ? >> let's say, at the first time, I run simulation with 3 nodes. A

Re: [gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

2016-04-17 Thread REMYA R
Yes sir, even though its not working On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/17/16 11:35 AM, REMYA R wrote: > >> Dear sir, >> >> I am getting error while running simulation of Protein-Ligand complex , >>

[gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

2016-04-17 Thread REMYA R
/complex_old/06_equil.html ) Here below I am pasting some information from em.log D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 48020.5 R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes

Re: [gmx-users] mdrun on multiple nodes

2016-04-20 Thread Husen R
il.com> wrote: > Hi, > > Probably you haven't built gromacs with MPI support, else the name of the > binary would be gmx_mpi. You can get that confirmed if you look further > down the output .log files. > > Mark > > On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com>

Re: [gmx-users] mdrun on multiple nodes

2016-04-20 Thread Husen R
gt; wrote: > Hi, > > Probably you haven't built gromacs with MPI support, else the name of the > binary would be gmx_mpi. You can get that confirmed if you look further > down the output .log files. > > Mark > > On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com>

[gmx-users] mdrun on multiple nodes

2016-04-20 Thread Husen R
Hi all, I tried to run mdrun on more than one node using the command available in this url http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html . The following is my sbatch job : ###SBATCH #!/bin/bash #SBATCH -J sim #SBATCH -o

Re: [gmx-users] mdrun on multiple nodes

2016-04-20 Thread Husen R
> Hi, > > Probably you haven't built gromacs with MPI support, else the name of the > binary would be gmx_mpi. You can get that confirmed if you look further > down the output .log files. > > Mark > > On Wed, 20 Apr 2016 10:09 Husen R <hus...@gmail.com> wrote: >

Re: [gmx-users] mdrun on multiple nodes

2016-04-20 Thread Husen R
ld all be along the lines of > > mpirun -np 2 gmx_mpi mdrun > > or > > mpirun -np 2 mdrun_mpi > > if the admins have done an mdrun-only installation. > > I'll fix that for future versions > > Mark > > On Wed, 20 Apr 2016 13:34 Husen R <hus...@gmail.com&g

[gmx-users] gmx xpm2ps

2017-03-31 Thread Kulkarni R
Hi gromacs users, After completing production run, I gave this command gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red However, I got error, --- Program: gmx xpm2ps, VERSION 5.1.1 Source file:

Re: [gmx-users] gmx xpm2ps

2017-03-31 Thread Kulkarni R
: [gmx-users] gmx xpm2ps On 3/31/17 11:27 AM, Kulkarni R wrote: > Hi gromacs users, > > > After completing production run, I gave this command > > > gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red > > > However, I got error, > > > ---

Re: [gmx-users] gmx xpm2ps

2017-03-31 Thread Kulkarni R
Subject: Re: [gmx-users] gmx xpm2ps "gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f hbmap.xpm -o hbplot.eps -rainbow red" You have a blanck space between the "-" and the "o". On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R <alumniph

Re: [gmx-users] LINEAR INTERACTION ENERGY

2017-03-16 Thread Kulkarni R
ynopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w] [-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ] Curr Comput Aided Drug Des. 2015;11(3):237-44. On Thursday, March 16, 2017 12:15 PM, Kulkarni R <alumniphys...@hotmail.com> wrote: Hi gromacs

Re: [gmx-users] COMMAND TO DISPLAY SIMULATION COMPLETION TIME

2017-03-16 Thread Kulkarni R
Thanks From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nikhil Maroli Sent: Thursday, March 16, 2017 7:41 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re:

[gmx-users] LINEAR INTERACTION ENERGY

2017-03-16 Thread Kulkarni R
Hi gromacs users, In order to calculate delta G (Gibbs free energy) for protein ligand binding, what are the steps to be followed in Linear interaction energy? Are there any tutorials for the same? Thanks, Kulkarni.R -- Gromacs Users mailing list * Please search the archive at

[gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

2017-03-31 Thread Kulkarni R
Hi gromacs users, After protein ligand simulations, I want to do energy analysis. How to interpret the following data properly? What books and papers should we refer? Energy AverageErr.Est. RMSDTot-Drift

[gmx-users] g_mmpbsa

2017-03-21 Thread Kulkarni R
Hi gromacs users, How to install mmpbsa using cgywin? I am using gromacs through cgywin. Thanks, Kulkarni.R -- 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

[gmx-users] Clayff forcefield

2017-08-02 Thread G R
I try to implement CLYFF in gromacs. I created ffbonded.itp, ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to create a topology. My first question is that should I create any other files?

[gmx-users] Could not find clayff forcefield

2017-08-04 Thread G R
Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1

[gmx-users] RDF

2017-07-11 Thread Vidya R
Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] TIP4P/ice pdb file

2017-07-06 Thread G R
list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. TIP4P/ice pdb file (G R) >

[gmx-users] TIP4P/ice pdb file

2017-07-05 Thread G R
Dear All, I would like to simulate water using TIP4P/ice potential. My question is that how can I generate .gro file for this simulation? I will use TIP4P/ice topology that is available in SklogWiki, but I cannot understand how can I generate .gro file for this topology. Can I easily use

[gmx-users] TOPOLOGY USING OPLS FORCEFIELD

2017-08-06 Thread Vidya R
Hi gromacs users, After getting the output from topolbuild, how to construct topology file using opls forcefield? Can anyone send useful links for the same? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

[gmx-users] compiling ambconv

2017-07-30 Thread Vidya R
Hi gromacs users, How to compile ambconv extracted from ambconv.tgz? Thanks, Vidya R -- 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/Support/Mailing_Lists

[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN

2017-08-08 Thread Vidya R
Hi, How to get good (and fast) performance from mdrun through available 8 logical CPU cores? When I gave, gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq It seems to be slow, much slower than gmx mdrun -v -deffnm eq. Can anyone help? Thanks, Vidya R -- Gromacs Users mailing list * Please search

[gmx-users] clayff forcefield

2017-08-07 Thread G R
Dear usres, I try to write clayff forcefield, and I want to simulate Kaolinite. I have some questions about it. 1) should I write clayff forcefield separately or modify one of the forcefields in share/top? 2) The directory for clayff forcefield should be included ffbonded.itp, ffnonbonded.itp,

[gmx-users] Simulation of pure water

2017-06-06 Thread G R
Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I

[gmx-users] Simulation of pure water

2017-06-07 Thread G R
Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I

[gmx-users] how to fix pme number

2017-09-15 Thread Vidya R
Hi gromacs users, In this command, gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2 how to determine the value of pme.. I want to include -npme... Please help Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx tune_pme

2017-09-15 Thread Vidya R
Hi gromacs users, When i tried using, gmx tune_pme -np 8 -s eql2.tpr -launch Got this error.. How to fix it? [compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105

[gmx-users] what is the difference between gmx mdrun and gmx tune_pme

2017-09-15 Thread Vidya R
Hi gromacs users, What is the difference between gmx mdrun and gmx tune_pme? Which is better to use in a cluster (especially when we submit our jobs through qsub command?) Also, what is the purpose of -np option in gmx tune_pme? Can someone elucidate? Thanks, Viday.R -- Gromacs Users

[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-16 Thread Vidya R
My log file is provided in the link below Can you please look into it and let me know why the error arises? I am feeding my commands in SGE cluster. When I run it in my login node, gmx mdrun -v -deffnm eql runs well But, through qsub command, (with 8 processors) It says, mpirun noticed that

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Vidya R
https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU /view?usp=sharing=59be86ad On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/17/17 1:22 AM, Vidya R wrote: > >> My log file is provided in the link below >> >> Ca

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Vidya R
whatever quirks exist with SGE are unfortunately between you, its docs and > your cluster's docs and admins :-( > > Mark > > On Sun, Sep 17, 2017 at 7:23 AM Vidya R <vidyadevi2...@gmail.com> wrote: > > > My log file is provided in the link below > > > > C

[gmx-users] selecting atoms in index file

2017-09-07 Thread G R
Dear All, I want to create an index file and select some especial atoms in a surface. My problem is that I have only one residue for the whole surface. How can I select the atoms on the surface as a different groups in my index file? Thank you in advance, Golnaz -- Gromacs Users mailing list *

Re: [gmx-users] selecting atoms in index file

2017-09-07 Thread G R
in my > index file, should I delete these atoms from surfaces groups. let me > explain better. Now I have 2 groups in my index file Sol and > Kaoli(surface). I should select some atoms from the Kaoli. So first I > define the atoms that I want to select in a seperate group, then I should > e

[gmx-users] gromacs error

2017-09-11 Thread Vidya R
Hi, When I give these two commands gmx grompp -f mdp/min.mdp -o min -pp min -po min gmx mdrun -deffnm min I get this error. What to do? Reading file min.tpr, VERSION 5.0.2 (single precision) tMPI error: tMPI Initialization error (in valid comm) Thanks, Vidya.R -- Gromacs Users mailing

[gmx-users] error sharing libraries...gromacs error

2017-09-12 Thread Vidya R
Hi, I give these commands PATH=$PATH:"/usr/local/gromacs/bin/" export GMXLIB=/usr/local/gromacs/share/gromacs/top export LD_LIBRARY_PATH=/usr/lib export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" export

Re: [gmx-users] error sharing libraries...gromacs error

2017-09-12 Thread Vidya R
use the > C++ performance is very poor. We recommend latest gcc or intel. > > Otherwise, configure GROMACS so that it uses the wrapper compilers when > buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ > etc. Organizing this stuff is their job. > > Ma

Re: [gmx-users] gromacs error

2017-09-12 Thread Vidya R
ted since. > Since a rebuild is the way to investigate that, definitely update to at > least the latest 5.0.x while you do it. > > Mark > > On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barn...@columbia.edu> > wrote: > > > On Mon, Sep 11, 2017 at

[gmx-users] DSSP

2017-12-04 Thread Vidya R
Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install dssp tool. How to proceed? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] DSSP

2017-12-05 Thread Vidya R
mailed Maarten at "m.hekkel...@cmbi.ru.nl" but I'm not sure this > email is active anymore. Hopefully it is, otherwise please let me know. > > Best regards, > J > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2...@gmail.com> wrote: > > > Hi gro

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