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

Dmitri Dubov ddubov at ngs.ru
Wed Jun 9 12:04:07 CEST 2010

Hi, Tsjerk.

Thanks for your help.

> 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. 
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.

> 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?

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