[gmx-users] protein jumps 10nm south in the ~20000th frame

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 11 11:21:02 CEST 2003

On Fri, 2003-04-11 at 11:07, Paul Barrett wrote:
> Id like to report odd behaviour in mdrun that I *suspect* is a bug.
> Im simulating a globular protein with a resident ATP and Mg2+. The
> system is water solvated with periodic boundary conditions.
> All goes well for the first couple of hundred thousand steps (2 fs
> steps) and then the problem arises.
> When the .xtc is viewed in VMD you see the whole protein jump (intact)
> about 10 nm "south" leaving the ATP and MG where they were. Other than
> that all is fine. This configuration stays for a few frames, then
> reverts to the correct config, only to lapse again a few frames later.
> This continues over a couple of hundred frames then seems to fix
> itself.
> I note that the amount it jumped was similar to the size of my unit cell
> for periodic boundary conditions. Maybe VMD is interpreting the two
> chains as being in neighbouring cells when the molecule has drifted out
> of the unit cell. ??? mdrun performs a MOD function happily bringing the
> calculations back in frame, but VMD looks at the bare un-MODed
> coordinates???? Just a guess.
> I plan to just delete the funnny frames. Makes me a bit nervous
> though...
> any comments?

this is just PBC in action. Does your box happen to be 10 nm ?

> Paul
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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