Re: [gmx-users] Regarding conversion of .trr file to readable file
Hi, You can use : *trjconv* -f yourtraj.trr -o output.gro -s input.tpr Regards, Bappa Ghosh IISER Pune, India On Thu, May 4, 2017 at 1:26 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > How can i convert a .trr/xtc file into a readable file format ..?? > How can it be done..?? since .trr/.xtc files are in binary format and i > want to convert it into a readable file format (eg., .gro format).. > > Thank you > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature=en; > referral=cy16f01.di...@nitk.edu.in=22> > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Adding external field to selected atoms
Dear users,
I am trying to add an external field which will add some extra force to my
simulation system for selected atoms.
For that, I was following the "patching mdrun" exercise in
http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun.
There it tells to replace the function calc_f_el in
gmx/src/mdlib/sim_util.c as follows-
for(i=start; (i<start+homenr); i++) {
if (x[i][ZZ] < box[ZZ][ZZ]/2) {
Ext[ZZ] = FIELDFAC*Ex[ZZ].a[0]*2*x[i][ZZ]/box[ZZ][ZZ];
}
else {
Ext[ZZ] = FIELDFAC*Ex[ZZ].a[0]*(1- 2*x[i][ZZ]/box[ZZ][ZZ]);
}
f[i][ZZ] += charge[i]*Ext[ZZ];
}
in order to add an external electric field along Z variable of the box.
My questions are-
1. What are the variables *"start" *and *"homenr" *mean ?
2. In order to add force by the external field to selected atoms, is there
any way to select atoms from the simulation system ( may be from the
index.ndx file ) which can be included here ?
Thank you in advance.
Best regards,
Bappa Ghosh
--
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
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
[gmx-users] Continuing simulation with velocities and positions of equilibrated run and after modifying .mdp
Hello All, I have a polymer chain of N=50. I equilibrate (NVT) the polymer for nsteps = 5 at T= 295K keeping only the N=1 positional restrained . After finishing the equilibration run, the production run is to be started lifting the positional restrain and applying a pull force on N=1 along Z-direction. My questions (A) Can I use the state.cpt file of the completed equilibration run to start my production from the same velocities and positions ? In this case, I have to modify .mdp file in two places for production run- (1) to lift the positional restrain on N=1 , I need to remove "define = -DPOSRES_N1". (2) to apply the pull force on N=1 , pull= constant_force pull_group1= N1 pull_dim= N N Y pull_k1 = 5 (B) Is there a way to check that I am starting from the same velocities and positions of the last equilibration frame ? I am using GROMACS-4.5.5 (single precision). Thank you in advance. Best regards, Bappa Ghosh -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem in extending simulation with state.cpt while changing number of cores
Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in extending simulation with state.cpt while changing number of cores
Thanks Mark for your reply, I am using gromacs version 4.6.3 with single precision. Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my typing mistake. So the command line was as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally started. Mark On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh ab54...@gmail.com wrote: Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
