[gmx-users] Re: Energy conservation of crystal surface(specification)

Berk Hess gmx3 at hotmail.com
Mon May 7 13:57:57 CEST 2007

>From: Janne Hirvi <janne.hirvi at joensuu.fi>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Re: Energy conservation of crystal 
>Date: Mon,  7 May 2007 14:44:34 +0300
> >>Hello again!
> >>
> >>In earlier message I said that double precision (actually same with 
> >>precision) simulation with 4 processors terminates pretty soon and 
> >>momentary increases in energy at intervals of 0.05ps can be observed 
> >>that point.
> >>
> >>Now I have made more tests and noticed that actually the time interval
> >>between these "energy steps" is connected to output control parameters - 
> >>least a value of nstxout has effect on the results. Multiple simulations 
> >>different values of nstxout (other parameters won't change and 
> >>gave different kind of energy curves. Energy values were equal at the
> >>beginning but deviated just after the time step, which coordinates were
> >>written to trajectory file. Energy always increases sharply at that 
>and >>equilibriates to the corresponding value until next sharp increase is
>observed >>when coordinates are written to trajectory file next time.
> >>
> >>This sounds pretty strange and I would like to know if there is some
> >>limitations for parallelization when using option pbc=full or if someone 
> >>good ideas what I might be doing wrong? That hopefully might also solve 
> >>overall energy conservation problem with this system.
> >>
> >>Thanks for your time,
> >>
> >>Janne
> >
> > This sounds like a bug.
> >
> > Why do you need pbc=full?
> > I assume you did not try without pbc=full?
>I supposed that I will need pbc=full option when I have crystal structure 
>consists of infinite polymer chains. At least when I tried to use pbc=xyz 
>the constructed topology I got warnings about 1-4 interactions at huge 
>which was larger than the 1-4 table size, but afterwards thinking I 
>got realistic energies for the starting configuration. So could there still 
>some problems with the topology which however seems working properly?
> > Could you file a bugzilla report, with a setup that produces jump
> > within short time?
> > Berk.
>I will send it tomorrow if you think that there is no explanation - I mean 
>if I
>haven't screwed up with these pbc options...

You can't screw up with pbc options.
And you can't have screwed up anythins else if you are sure that the jump
move along with nstxout and you have not changed any other parameter.

I assume this problem is not related with double precision and that it would
also occur in single precision.


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