Thanks! It really is. For the input cpt may have been overwritten before, when I put it in mdrun again..
2010/12/17 Mark Abraham <mark.abra...@anu.edu.au> > > > On 12/17/10, *Qin Qiao * <qiaoqi...@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 <jalem...@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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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