[gmx-users] more than one peptide in one simulation box

shahid nayeem msnayeem at gmail.com
Fri Apr 23 05:16:20 CEST 2010

Dear All
I am trying to study inter peptide interaction fpr which I need to put more
than one peptide in one simulation box. I did it with genconf command but
this inserts peptide in a regular ordered manner I want these to be in
irregular disordered insertion. Even after using genconf , I tried to
proceed furthe after solvation with spc water. The energy minimization
(steepest descent) failed to converge even after 5000 steps and theirafter
position restraint dynamics failed giving segmentation fault. Introducing
more peptide after generating .gro with -ci -nmol gives error showing more
than one residue in insert molecule.
Please help me and write  commands which I should follow.
Shahid Nayeem
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100423/aa160f88/attachment.html>

More information about the gromacs.org_gmx-users mailing list