[gmx-users] Extending Simnulation - how analyze?

[Mark Abraham]

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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