[gmx-users] Question about Extention simulation in REMD

[Mark Abraham]

On 12/17/10, Qin Qiao  <qiaoqin47 at gmail.com> wrote:
> Thanks! 
> 
> But still sth strange: I found the total energy is not identical between the last frame of the previous REMD and the first frame of the next REMD in one replica. 
> 
> last frame of the previous: 500.000000  -372343.906250
> 
> first frame of the next:          0.000000  -361778.375000
> 
> I wonder whether there's some problem and what caused it..
> 

OK, we'll need to see the exact sequence of commands that produced your observations, i.e. mdrun, then tpbconv, then mdrun. The fact that you're managing to get the time reset to zero indicates you've done something wrong. As a guess, you didn't use the right .cpt file with the second mdrun -cpi.


> 
> 
> My setting
> In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. 
> 

These don't matter.

Mark


> 
> Best
> 
> Qin
> 
> 2010/12/15 Justin A. Lemkul <jalemkul at vt.edu>
> 
> > 
> > 
> > 
> > 
> > 
> > 
> > Qin Qiao wrote:
> > 
> > 
> > > 
> > > Dear Sir or Madam,
> > > 
> > > 
> > > 
> > > I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by
> > > 
> > > 
> > > 
> > > tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> > > 
> > > 
> > > 
> > > mdrun -s next.tpr -cpi previous.cpt
> > > 
> > > 
> > > 
> > > 
> > > 
> > > I guess it's not for an iterative line in the answer in http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since the mdrun should run simultaneously.
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > 
> > The iterative approach Mark describes in that post is for the tpbconv step. Simply extend all of your .tpr files to generate new ones (iterate over all your .tpr files), then proceed with mdrun as you would normally, making use of the -cpi feature.
> > 
> > 
> > 
> > 
> > -Justin
> > 
> > 
> > 
> > 
> > > 
> > > Could you give some advice? Thanks.
> > > 
> > > 
> > > 
> > > Best,
> > > 
> > > 
> > > 
> > > Qin
> > > 
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > -- 
> > 
> > ========================================
> > 
> > 
> > 
> > Justin A. Lemkul
> > 
> > Ph.D. Candidate
> > 
> > ICTAS Doctoral Scholar
> > 
> > MILES-IGERT Trainee
> > 
> > Department of Biochemistry
> > 
> > Virginia Tech
> > 
> > Blacksburg, VA
> > 
> > jalemkul[at]vt.edu(http://vt.edu) | (540) 231-9080
> > 
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > 
> > 
> > 
> > ========================================
> > 
> > -- 
> > 
> > gmx-users mailing list    gmx-users at gromacs.org
> > 
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 
> > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > 
> > Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> > 
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> > 
> 
> 
> 
> 
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101217/9fffb4a9/attachment.html>