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

Janne Hirvi janne.hirvi at joensuu.fi
Mon May 7 13:44:34 CEST 2007

>>Hello again!
>>In earlier message I said that double precision (actually same with single
>>precision) simulation with 4 processors terminates pretty soon and distinct
>>momentary increases in energy at intervals of 0.05ps can be observed until 
>>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 - at
>>least a value of nstxout has effect on the results. Multiple simulations with

>>different values of nstxout (other parameters won't change and nstenergy=1)
>>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 moment
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 has
>>good ideas what I might be doing wrong? That hopefully might also solve my
>>overall energy conservation problem with this system.
>>Thanks for your time,
> 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 which
consists of infinite polymer chains. At least when I tried to use pbc=xyz for
the constructed topology I got warnings about 1-4 interactions at huge distance
which was larger than the 1-4 table size, but afterwards thinking I actually 
got realistic energies for the starting configuration. So could there still be
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...


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