From: Janne Hirvi <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Energy conservation of crystal
surface(specification)
Date: Mon, 7 May 2007 14:44:34 +0300
>>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,
>>
>>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
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...
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.
Berk.
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