[gmx-users] Extending Simnulation - how analyze?

[Mark Abraham]

Hi,

Was that actually your mdrun command line? I think you need

gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append)

to actually get appending happening. mdrun does not deduce the names of the
output files from the contents of the checkpoint file.

Mark

On Tue, Jul 14, 2015 at 9:47 AM Andrea Spinelli <spinelli87 at gmail.com>
wrote:

> Hi Mark,
> in the .log file there are this lines at the start of the extending.
>
> There are: 20587 Atoms
> Charge group distribution at step 500000: 5190 5166 5109 5122
> Initial temperature: 319.123 K
>
> Started mdrun on rank 0 Sun Jul 12 20:50:29 2015
>            Step           Time         Lambda
>          500000     1000.00000        0.00000
>
>
>
> On Jul 14, 2015, at 9:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli <spinelli87 at gmail.com>
> > wrote:
> >
> >> @Mark
> >> The .log report works for 2000 ps.
> >>
> >
> > Sure, but you need to look at the bit between 1 ns and 2 ns to find out
> > what happened when you attempted to append.
> >
> > Mark
> >
> >
> >> @Chaban
> >> I not use grompp and the extension not create .trr files.
> >>
> >> What I have to do?
> >>
> >> On Jul 14, 2015, at 3:56 AM, V.V.Chaban <vvchaban at gmail.com> wrote:
> >>
> >>> The no-headache route is:
> >>>
> >>> mv confout.gro conf.gro
> >>> grompp
> >>> mdrun
> >>> trjcat -f *.trr -o fixed.trr
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham <
> mark.j.abraham at gmail.com>
> >> wrote:
> >>>> Hi,
> >>>>
> >>>> What did the .log file report about your attempt to append?
> >>>>
> >>>> Mark
> >>>>
> >>>> On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli <
> spinelli87 at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> Hi,
> >>>>> I’m new user of Gromacs and I need extend a simulation of 1000ps.
> >>>>> On Gromacs 5.0.5 I use this command line as tutorial said.
> >>>>>
> >>>>> gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
> >>>>> gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append
> >>>>>
> >>>>> It produced the md_0_2.tpr , but when I run rms command to watch the
> >> state
> >>>>> of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why?
> >>>>> What is the command I have to use?
> >>>>>
> >>>>> to view rmds I use this command line:
> >>>>> gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg
> >>>>>
> >>>>> Thanks a lot.
> >>>>>
> >>>>>
> >>>>> Andrea Spinelli
> >>>>>
> >>>>> Please do not print this email unless really need to.
> >>>>> Save paper, save trees, save space, save money - life matters.
> >>>>>
> >>>>> --
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> Andrea Spinelli
>
> Please do not print this email unless really need to.
> Save paper, save trees, save space, save money - life matters.
>
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