[gmx-users] Non-conservation of total energy while using structure file to resume the simulation

[Tsjerk Wassenaar]

Hi Dmitri,

Try

editconf -f your_run_input_file.tpr -o test.gro

to see if the box is stored correctly in the .tpr. Alternatively, you
can do gmxdump -s your_run_input_file.tpr, and browse for the box in
the output. Then, see if you can reproduce the problem with the last
frame of the .trr file extracted, and consider submitting a bugzilla.

Cheers,

Tsjerk

On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov <ddubov at ngs.ru> wrote:
> First, sorry for the revival of this thread so late (maybe it should be
> better to start a new one).
>
>> ----- Original Message -----
>
>> From: Dmitri Dubov <ddubov at ngs.ru>
>
>> Date: Thursday, May 27, 2010 19:11
>
>> Subject: Re[2]: [gmx-users] Non-conservation of total energy while
>
>> using structure file to resume the simulation
>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>>> > I expect that either
>
>>> > grompp -f new -o newtpr
>
>>> > mdrun -s newtpr -cpi old_state.cpt
>
>>> No, this way is unsuccessful, maybe due to somewhat contradictive
>>> instructions:
>
>>> grompp supplies newtpr with usual options
>
>>> tinit                    = 0
>
>>> nsteps                   = 100000
>
>>> simulation_part          = 1
>
>>> and from old_state.cpt the system finds itself on 100000th step already
>>> and stops.
>
>> OK. Presumably some more cunning choice of .mdp options would work,
>
>> or using grompp, tbconv -extend and then mdrun.
>
>>> > grompp -f new -t old_state.cpt -o newtpr
>
>>> > mdrun -s newtpr
>
>>> > will do what you want. Please report back if one or both work :-)
>
>>> And the latter variant is working! More precisely I use
>
>>> grompp -f new -t old_state.cpt -c oldtpr -o newtpr
>
>>> mdrun_d -s newtpr
>
>> Mark
>
> But I have noted just now that using grompp with -t option results in some
> bug: after simulation right size of my cubic box (last line of input
> structure file)
>
>   10.00000  10.00000  10.00000
>
> changes in confout.gro to meaningless
>
>    0.00000   0.00000   0.00000
>
> To analyse the output properly (e.g. with g_rdf tool) I have to correct this
> line manually.
>
> And I'm worried whether this bug effects to my simulation itself, during md
> integration of NVE ensemble in vacuum?
>
> --
>
> Rerards,
>
>  Dmitri                          mailto:ddubov at ngs.ru
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands