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

Mark Abraham mark.j.abraham at gmail.com
Mon Mar 10 17:41:13 CET 2014

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.


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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