[gmx-users] Re: problem with dimer simulation !

[David van der Spoel]

C.W. Liang wrote:
> try - cluster, and then as cluster group protein.
> Kay.
> hello, Kay
>  
> thanks so much for your advice, but with -pbc cluster, one of the two 
> peptides still move out of the box and frequently jump back.
> i have no idea about it, any else should i do ?
>  

merge the peptides into one protein (pdb2gmx -merge) and make a distance 
restraint between them with distance much larger than the actual 
distance. you only need to do this for post-processing the output, not 
for the simulation.


> best regards,
>  
> Liang
>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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