Dear gromacs users, I want to do md similation of 10 small molecules in water. To this aim, I used following commands:
gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb gmx_mpi insert-molecules -ci b.pdb -o c.gro -nmol 10 -box 10 10 10 I have 3 questions: 1) Is my manner true? 2) For 10 molecules, which dimention of box is appropriate? 3) When I see c.gro using vmd, the part of some molecules are put out of box. https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/4MQPVS000T2QS0057UNJ7CHP22TZF9G9/c.gro https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/TZKXARG00T2QS0057UNJK110Y2TZF9GM/c.jpg Please guide me about that. Best, Shahab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
