Re: [gmx-users] can not write coordinate file when running ibi

Dear Zhichen, This is not the appropriate forum for your query. It seems you are using votca for coarse grained simulations. Please post at votca@googlegroups.comrelating all your votca queries. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Nov 18, 2013 at 10:49 AM, cqgzc

Re: [gmx-users] energy group tables

On Mon, Nov 25, 2013 at 11:22 PM, Humberto Saint-Martin xibas...@gmail.comwrote: Hi, Chandan, Within the *.mdp file you have to write the pairs without hyphens. Following your example, if you specify energygrps = A B C then the tables should be declared as folows: energygrp_table = A

Re: [gmx-users] mdrun_mpi_d

Dear Eslami, Gromacs 4.6.3 can automatically take up all the cores. If you want to run gromacs across the nodes. Then you need to compile using MPI. Detailed instruction is available here http://www.gromacs.org/Documentation/Installation_Instructions. Chandan -- Chandan kumar Choudhury NCL,

Re: [gmx-users] GMX_THREAD_MPI=ON does not exis

On Sat, Nov 30, 2013 at 1:22 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: Thank you for your help What command do I use to use 8 cores mdrun -nt 8 -s *.tpr or mpirun -np 8 mdrun_mpi -s *.tpr Chandan Good luck -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] out of disk space error

Dear vaani, Please rerun the gmx executable. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote: hi chandan.. output for ls -1 is as follows: the directory from where i am running simulatons is in desktop .. and i have

Re: [gmx-users] out of disk space error

Dear vaani, Sorry for the unclear message. Try running the mdrun command once again and post the out put of the log file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote: i am sorry ..but i kind of dint get you .. -

[gmx-users] simulation using tabulated dihedral potentials.

I am facing some weird problem while using tabulated potentials (esp. dihedral tabulated potentials) in gromacs 4.6.3. I am trying to generate a coarse grained (CG) trajectory using the tabulated potentials generated for the atomistic simulations using VOTCA. When I donot use the dihedral

Re: [gmx-users] simulation using tabulated dihedral potentials.

On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Do your tabulated functions work on a toy system, like butane? No Mark. I didnot try with butane. The simulation stops when I incorporated tabulated dihedral potential. Chandan -- Chandan kumar Choudhury NCL, Pune

Re: [gmx-users] simulation using tabulated dihedral potentials.

On Mon, Dec 9, 2013 at 6:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/9/13 8:09 AM, Chandan Choudhury wrote: On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Do your tabulated functions work on a toy system, like butane? No Mark. I didnot try

Re: [gmx-users] Fw: Error in extendig md run in gromacs

On Sat, Dec 14, 2013 at 10:52 AM, Keerthana S.P Periasamy keerthanas...@yahoo.com wrote: On Saturday, December 14, 2013 10:51 AM, Keerthana S.P Periasamy keerthanas...@yahoo.com wrote: Hai initially I used 4processors for mdrun and due to some power fluctuations i have

Re: [gmx-users] simulation using tabulated dihedral potentials.

Abraham mark.j.abra...@gmail.comwrote: Agreed. I would suggest varying which of the tables are used, to find a culprit. Mark On Dec 11, 2013 1:46 AM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Dec 10, 2013 at 4:47 AM, Chandan Choudhury iitd...@gmail.com wrote: On Mon, Dec 9, 2013

Re: [gmx-users] simulation using tabulated dihedral potentials.

On Sat, Dec 28, 2013 at 5:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/27/13, 12:58 AM, Chandan Choudhury wrote: Dear Justin and Mark, Thanks for the reply. I have regenerated the potentials for the bonded and non-bonded part. I observe the similar behavior as previous. Keeping

Re: [gmx-users] Combine parts

On Tue, Feb 25, 2014 at 4:45 PM, Hassan Aaryapour hassan.grom...@gmail.comwrote: Dear Gmx-user; How can I combine parts of my simulation after final MD? The results of my MD are splitted to several parts with .tgz format. Dear Hassan, Gromacs trajectories are written in .trr or .xtc

Re: [gmx-users] Can't make links on GROMACS

On Fri, May 9, 2014 at 6:11 PM, Ooker ganuongp...@gmail.com wrote: I mean that it is a bug because you can't make link after build from the source, although it is easy to work around with it. If you are not the super user, you cannot make links. -- Gromacs Users mailing list * Please

Re: [gmx-users] water stretched apart

Dear Chetan, trjconv is finding difficult to find the trp file. Check that the tpr yourare providing is in the right place. Chandan On Sun, May 11, 2014 at 1:33 PM, Chetan Mahajan chetanv...@gmail.comwrote: Thanks, Tsjerk. I tried it with following: trjconv -pbc whole -f lnanop.xtc -s

Re: [gmx-users] topology in local?

Dear Nicola, Any number of users can use the top directory, with the choice of his/her force field. If anyone wants to edit the top files, then he can copy the top directory to somewhere and use the GMXLIB variable. You can use the GMXLIB environment variable, and point your top directory's path

Re: [gmx-users] topology in local?

On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

On Wed, May 21, 2014 at 6:37 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution.

Re: [gmx-users] RDF of solvation shell molecules

Hi Sujith, g_rdf is the tool you need. Chandan On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.comwrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect

Re: [gmx-users] Gromacs for reverse transformation

Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that

Re: [gmx-users] Gromacs for reverse transformation

problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward

[gmx-users] g_polystat sorts the eigen vector

Dear gmx users, The g_polystat tool arranges the Rg eigen vectors in the descending order. We cannot see how a particular eigen vector (one along the X-axis) varies with time. We can obviously comment the section of the g_polystat code to avoid the sorting. Is there a reason, why do we sort the

Re: [gmx-users] g_polystat sorts the eigen vector

Dear gmx users, In my previous mail, please read eigen vectors as eigen values. The command used was $echo 3 | g_polystat -s md0-1.tpr -f traj.xtc -b 50 -n poly.ndx -o 3.xvg I am using v4.6.3. Sorry for the misleading information. Thanks On Thu, Jul 3, 2014 at 2:35 AM, Chandan Choudhury

Re: [gmx-users] error in grompp command

Dear Rinu, You need to arrange the gro file is the same sequence as in the top file (or the vice-versa). Chandan On Thu, Jul 3, 2014 at 3:57 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello gromacs users now have been removed this error after changing the number of SOL in

Re: [gmx-users] GPU tutorial

Dear Raman, 1. For using GPU enabled gromacs, the gromacs must be installed using -DGMX_GPU=ON flag. 2. The commands are all same as with the non gpu enabled ones. For running the mdrun program, you need to incorporate cutff-scheme = verlet in the mdp file (Details can be viewed at

Re: [gmx-users] more than 99,999 atoms in conf.gro

Hi Sikandar, Did you try resetting your atom number to 1 as it reaches 10? I hope this would resolve the issue. Chandan On Tue, Jul 15, 2014 at 3:43 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am trying to run a simulation with more than 99,999 atoms in a conf.gro file.

Re: [gmx-users] how to write in a script?

Dear Albert, You can have a look at the following page http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Chandan On Thu, Aug 7, 2014 at 4:29 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to make a workflow of system building steps of gromacs. However, many

Re: [gmx-users] Regarding gromacs installation

Follow this link http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.11._Getting_access_to_GROMACS_after_installation Chandan On Thu, Sep 4, 2014 at 10:32 AM, Sathya bti027.2...@gmail.com wrote: Hi I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS. During

Re: [gmx-users] undefined symbol: TMPI_BYTE

, Sep 13, 2014 at 3:09 PM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, Following error pops up when I try to run mdrun (v4.6.6) $ mdrun_466 -h mdrun_466: symbol lookup error: mdrun_466: undefined symbol: TMPI_BYTE Can anyone suggest me the workaround to this? I have

Re: [gmx-users] How can I select a group number automatically

Use echo $echo 0 | g_msd -s topol.tpr -f traj.xtc Chandan On Wed, Sep 24, 2014 at 9:35 AM, Xiaobin Cao x...@lsu.edu wrote: Hi Gromacs users, When I do msd analysis (g_msd), there is a promotion to select a group number. I am wondering how can I select a number using a script. So the

[gmx-users] Different fudge scaling against the default ones

Dear gmx users, I see the following lines in the forcefield.itp file of amberGS.ff (gmx 466) (share/gromacs/top/amberGS.ff/) : ;-- #define _FF_AMBER #define _FF_AMBER94 [

[gmx-users] force-switch as vdv-modifier

Dear gmx users, I was trying to use the Force-Switch as the vdv-modifier with Verlet cutoff scheme. The use of Force-Switch produces the following error: *ERROR 1 [file grompp.mdp, line 63]: Invalid enum 'force-switch' for variable vdw-modifier, using 'Potential-shift-Verlet' Next time

Re: [gmx-users] force-switch as vdv-modifier

in Gromacs 5 Mark On Wed, Oct 29, 2014 at 8:06 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear gmx users, I was trying to use the Force-Switch as the vdv-modifier with Verlet cutoff scheme. The use of Force-Switch produces the following error: *ERROR 1 [file

Re: [gmx-users] Version problem

Dear Satya, GMXRC is present in the installation directory. You need to find where you have installed the gromacs 5.0.2. Then locate the bin directory. GMXRC is generally present there. Chandan On Thu, Nov 6, 2014 at 2:00 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner,

Re: [gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)

Dear Amit, I do not have the solution of this problem. I have also encountered the similar error. What I do to avoid such thing, is (a) I run simulation in steps of shorter time (say 50 ns). (b) Then continue the simulation for larger times using the cpt file (

Re: [gmx-users] Doubt regarding nrexcl parameter in topology

Dear Bipin, With nrexcl = 3 it excludes neighbours 3 bonds away, in this case your (ii) option falls. But an extra LJ and electrostatic interactions, is added between 1-4 pairs, if gen-pair is yes for the force field. These interactions are scaled by their respective fudge factor. For gromos ff,

[gmx-users] template parallelization

Dear gmx users, I am trying to parallelize execute the template (gmx 4.6.3), but unable to do so. When I just include the header file of mpi #includempi.h in the header section of template, and then compile (export CC=mpicc; make -f Makefile), it generates a lot of error: Output: mpicc

Re: [gmx-users] translate problem

Dear Jlom, If you need to translate along Z, then use -translate 0 0 -10 with your editconf command. Your command seems to translate along x. Chandan On Mon, Mar 2, 2015 at 5:16 PM, gromacs query gromacsqu...@gmail.com wrote: Hi All, I have membrane thickness along Z and want to merge

Re: [gmx-users] How I extend command?

use -cpi state.cpt in the mdrun command Replace state.cpt file with the actual cpt file written by mdrun. On Tue, Feb 24, 2015 at 10:39 AM, Abid Channa abid.cha...@hotmail.com wrote: Hi gromacs users, I am working membrane complex simulation of 20 ns, 100, steps , my simulation is

Re: [gmx-users] Force field parameterization for PAMAM dendrimers

Dear Farideh, We have recently published an article on PAMAM dendrimers. We used oplsaa forcefield. You can access the paper at http://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm00854a. Hope it helps. Chandan On Mon, May 18, 2015 at 12:58 PM, faride badalkhani

Re: [gmx-users] g_msd and Diffusion Constant

Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban vvcha...@gmail.com wrote: which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM,

Re: [gmx-users] g_msd and Diffusion Constant

to be round up. On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury iitd...@gmail.com wrote: Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM

Re: [gmx-users] Atomic charges

Which force field are you using? How did you obtain the charges? OPLSAA has its own charges., which can be modified for new molecules. Chandan On Wed, Sep 16, 2015 at 9:57 AM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello users, > > I have this confusion regarding the

Re: [gmx-users] Does .xtc enough for all kind of analysis?

trr also contains velocities and forces. Chandan On Thu, Sep 10, 2015 at 11:18 AM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi everyone, > Just has a general doubt. Does compressed coordinate file (.xtc) enough for > all kind of analysis? If so then why we need a large

Re: [gmx-users] no domain decomposition

Hi! Sometime decreasing the total number of nodes serves the purpose. Did you try decreasing the total number of nodes? Chandan On Sun, Sep 27, 2015 at 8:00 PM, soumadwip ghosh wrote: > Hi all, > I am simulating a DNA encapsulated in a carbon nanotube in the

Re: [gmx-users] No domain decomposition

g_tune_pme would give some useful information. On Mon, Sep 28, 2015 at 6:05 PM, soumadwip ghosh wrote: > Hi Chandan, > I tried it once using -nt option but it failed . I > kept it 8 although I dont know how to change the number of nodes for > mdrun

Re: [gmx-users] Extending simulations

Hi Soumya, I think you also need to mention -cpi state.cpt flag in the tpbconv command. Chandan On Mon, Dec 21, 2015 at 9:00 AM, Soumya Lipsa Rath wrote: > Dear Gromacs users, > > I am trying to extend my simulation for 200ns by using: > > tpbconv_mpi -s topol.tpr

Re: [gmx-users] combine two pdb files

You can try using editconf with resnr 1. On Nov 28, 2015 3:57 AM, "Peter Stern" wrote: > AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file since > in any case it reorders them and renumbers them after adding hydrogen > atoms. Did you try it? > >

Re: [gmx-users] Calculating avergae structure from the simulation

gmx rmsf -f *.xtc -s *.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res This would give you a average structure. On Wed, Jun 8, 2016 at 5:21 PM, Agnivo Gosai wrote: > Dear Users > > I had run an unrestrained 50 ns simulation of a protein-ligand

Re: [gmx-users] Lipid Head group Orientation

Hi Nidhin! I wrote a code some time ago on the the orientation of lipid molecules which was the specific to the problem addressed at http://pubs.acs.org/doi/full/10.1021/bm4011408. If you need, I can share. Chandan On Thu, May 26, 2016 at 7:50 PM, Nidhin Thomas

Re: [gmx-users] water permeation -using GROMACS

Hi Nikhil, I had written a code for this analysis. You can find its reference at http://pubs.acs.org/doi/abs/10.1021/bm4011408 Chandan On Tue, Jul 19, 2016 at 5:52 AM, Nikhil Maroli wrote: > Dear all, > > How can one calculate the number of water/ion molecules passing per

Re: [gmx-users] converting .gro trajectory to .pdb

Hi! You can try trjconv. On Wed, Jan 18, 2017 at 10:14 AM, Irem Altan wrote: > Hi, > > I have a trajectory saved in .gro format. It has multiple frames/snapshots > in it. I’m using .gro format because I needed higher precision than > standard .pdb precision, but now I can’t