Re: [gmx-users] mdrun with append option

Sai Pooja wrote: Thanks Justin for being so patient. I have understood almost everything and I hope this is the last question on this thread. See inline ... On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul > wrote: Sai Pooja wrote: On Wed, Feb 2, 2011

Re: [gmx-users] mdrun with append option

On Wed, Feb 2, 2011 at 6:49 PM, Sai Pooja wrote: > Thanks Justin for being so patient. I have understood almost everything and > I hope this is the last question on this thread. > > See inline ... > On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul wrote: > >> >> >> Sai Pooja wrote: >> >> On We

Re: [gmx-users] mdrun with append option

Thanks Justin for being so patient. I have understood almost everything and I hope this is the last question on this thread. See inline ... On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > mark.abra...@anu.edu.au>>

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > wrote: On 3/02/2011 6:15 AM, Sai Pooja wrote: The problem is solved with grompp i.e. I use the -t .cpt option. However, now appending does not work. I remember Mark said in a

Re: [gmx-users] mdrun with append option

On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham wrote: > On 3/02/2011 6:15 AM, Sai Pooja wrote: > >> The problem is solved with grompp i.e. I use the -t .cpt option. However, >> now appending does not work. I remember Mark said in a previous mail that a >> certain environment variable can allow appen

Re: [gmx-users] mdrun with append option

On 3/02/2011 6:15 AM, Sai Pooja wrote: The problem is solved with grompp i.e. I use the -t .cpt option. However, now appending does not work. I remember Mark said in a previous mail that a certain environment variable can allow appending to happen even in such cases. I would liek to try that ou

Re: [gmx-users] mdrun with append option

The problem is solved with grompp i.e. I use the -t .cpt option. However, now appending does not work. I remember Mark said in a previous mail that a certain environment variable can allow appending to happen even in such cases. I would liek to try that out. -- gmx-users mailing listgmx-users@

Re: [gmx-users] mdrun with append option

Mark Abraham wrote: On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Where was that? It could u

Re: [gmx-users] mdrun with append option

On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Where was that? It could use clarification. Mark So

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. So use grompp, as I suggested before. Using gmxdump to verify the number of atoms is also not what I suggested; it c

Re: [gmx-users] mdrun with append option

When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. Reading toplogy and stuff from rex_1.tpr Reading file rex_1.tpr, VERSION 4.5.1 (single precision) NOTE: Reading the state from trajectory is an

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates

Re: [gmx-users] mdrun with append option

I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Are you changing the integrator, ensemble, and/or other settings? I

Re: [gmx-users] mdrun with append option

>From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this as

Re: [gmx-users] mdrun with append option

Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abr

Re: [gmx-users] mdrun with append option

On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exc

Re: [gmx-users] mdrun with append option

I manually index checkpoint files after every mdrun. What troubles me is the randomness with which -append fails/works. For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun. Now oddly enough, the logfile starts from 1184ps(in the end, I do remember the one starting from 0 but that was o

Re: [gmx-users] mdrun with append option

I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exchanged cptfile. It seems that whenever the

Re: [gmx-users] mdrun with append option

On 30/01/2011 10:39 AM, Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. As I suggested a few ema

Re: [gmx-users] mdrun with append option

Disregard the version question; I see it now in the command string. You should still check for errors, and consider using version 4.5.3 to see if the issue persists. -Justin Justin A. Lemkul wrote: Sai Pooja wrote: I would be happy to supply more information.. if someone could please lo

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. In theory, there's nothing wrong with what y

Re: [gmx-users] mdrun with append option

I would be happy to supply more information.. if someone could please look into this.. otherwise I will have to switch to storing every file and then just concatenating them which seems like a rather roundabout way of doing it. On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja wrote: > This is the comm

Re: [gmx-users] mdrun with append option

This is the command: nbs submit -command "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap pend -g rexlog3 -x rextraj3);" -nproc 1 -name "GENHAM-DIHEDRAL-3" -mail start end Pooja On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham wrote: >

Re: [gmx-users] mdrun with append option

On 29/01/2011 3:56 AM, Sai Pooja wrote: Hi, I am using tpbconv and mdrun to extend a simulation. I use it with the append option but the files still get overwritten or erased. Can someone help me in this regard? Pooja Commands (in python) cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.t