[gmx-users] Energy conservation of crystal surface (specification)
gmx3 at hotmail.com
Mon May 7 11:43:00 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] Energy conservation of crystal surface (specification)
>Date: Mon, 7 May 2007 12:25:17 +0300
>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
>Now I have made more tests and noticed that actually the time interval
>these "energy steps" is connected to output control parameters - at least a
>value of nstxout has effect on the results. Multiple simulations with
>values of nstxout (other parameters won't change and nstenergy=1) gave
>different kind of energy curves. Energy values were equal at the beginning
>deviated just after the time step, which coordinates were written to
>file. Energy always increases sharply at that moment and equilibriates to
>corresponding value until next sharp increase is observed when coordinates
>written to trajectory file next time.
>This sounds pretty strange and I would like to know if there is some
>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
>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?
Could you file a bugzilla report, with a setup that produces jump
within short time?
Play online games with your friends with Messenger
More information about the gromacs.org_gmx-users