[gmx-users] Brownian dynamics]

[David van der Spoel]

On 13 Feb 2002, Michel Fodje wrote:

>> Isn't a timestep of 1 ps a bit much? Try 0.005 (5 fs)
>> 
>I tried a timestep of 0.005 but the result was the same.  Even 0.001 did
>not help. 
>
>Maybe I should mention that I also get a warning at the beginning which
>says 
>
>step 0Warning: 1-4 interaction at distance larger than 1
>These are ignored for the rest of the simulation
>turn on -debug for more information
If you do mdrun -debug it will tell you which atoms are taken apart.
It seems like you either have an incorrect topology or a start structure 
with bad contacts. Try some minmization before you start dynamics/

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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