[gmx-users] Problem in extending simulation with state.cpt while changing number of cores

[Bappa Ghosh]

Thanks Mark for your reply,

I am using gromacs version 4.6.3 with single precision.
Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my
typing mistake.
So the command line was as follows-

tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr
mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt





On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Please always report at least your GROMACS version!
>
> tpbconv does not take a -cpi argument, so if that is really your command
> line, then it is not doing what you think it is doing. Then mdrun has no
> option but to re-start from the only frame it knows about - the one from
> which you originally started.
>
> Mark
>
>
> On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh <ab54741 at gmail.com> wrote:
>
> > Hello all,
> >
> > I was simulating a mixture of water and carbon-di-oxide for 20ns in one
> > node with 32 cores. After completion of 20ns run' I extended it for
> further
> > 15ns with  tpbconv as follows-
> >
> > tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt
> > mdrun -s 15ns_new.tpr -o last_15ns.trr
> >
> > The last 15ns run was carried out in one node with 12 cores.
> > When I plot coulomb potential energy (short range) for whole 35ns
> > trajectory, I observe a sharp rise at the extention time (i.e at the
> > begining of last 15ns run). This sharp rise is not observed if the number
> > of cores are kept same during extension.
> >
> > Any comments/suggestions on this observation will be beneficial to me.
> >
> > Thanks in advance.
> >
> >
> > Bappa Ghosh
> > Project Student
> > ......................................
> > C/O -Dr Sudip Roy
> > Scientist,
> > CSIR-National Chemical Laboratory,
> > Pune-411008,India
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