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

Berk Hess 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
>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 
>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?


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