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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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