Thank you for the reply, Berk. But I would like to keep the two molecules in separate moleculetypes, which allows me to use the couple-moltype option for decouple the interactions between them. In this situation, is there any way to apply intermolecular distance restraint between atoms on two moleculetypes? Perhaps using the pull code (umbrella sampling) somehow? Many thanks for your suggestions,
Warren Berk Hess to me show details 5:07 PM (20 minutes ago) Reply fromBerk Hess <[email protected]> [email protected] dateTue, Apr 14, 2009 at 5:07 PM subjectRE: intermolecular distance restraint mailed-byhotmail.com hide details 5:07 PM (20 minutes ago) Reply Hi, Use pdb2gmx -merge to merge the moleculetypes. Please send Gromacs questions to the gmx-users list. Berk Date: Tue, 14 Apr 2009 12:13:10 +0800 Subject: intermolecular distance restraint From: [email protected] To: [email protected] - Show quoted text - Hi, Dr. Hess, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule types in Gromacs? Many thanks, Warren Express yourself instantly with MSN Messenger! MSN Messenger
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