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

[Dmitri Dubov]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100609/14025a77/attachment.html>