[gmx-users] Minimization of a box of capped tryptophan (trp)
David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 25 20:34:15 CEST 2007
OZGE ENGIN wrote:
> Hi all,
> As you suggest David I used genconf command without -rot option. I minimized a single capped trp molecule and got the minimized molecule and used that molecule with genconf command in order to create a box.
>> Then, I solvated capped trp molecule within the created box with genbox command. I wanted the box to have a total of 200 capped trp molecules. In this respect, I used -maxsol 200 option. However, the resultant system had only 11 capped trp molecules.
>> What may be the problem?
box too small?
use genconf -nbox 8 5 5 or something like that
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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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