[gmx-users] Non-conservation of total energy while using structure file to resume the simulation
ddubov at ngs.ru
Wed Jun 9 12:04:07 CEST 2010
Thanks for your help.
> 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.
Yea, both tests show "zero" box right in .tpr file!
> Then, see if you can reproduce the problem with the last
> frame of the .trr file extracted,
I'm afraid I cannot do it quickly...
For the future: I used double-precision mode,
how much should be the precision (-ndec) of the extracted frame?
> and consider submitting a bugzilla.
> 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: [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
>>>> 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
>> 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?
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