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

[Paul Barrett]

thanks david

yes (as I wrote) the jump is about the size of my box (9nm).

looks like I have to just live with it for my visualisation.

Paul



>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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