Dear Huey Ling, In principle it is applicable. Then such REMD can be termed as Hamiltonian REMD instead of canonical temperature REMD.
Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg ________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huey Ling Tan Sent: Tuesday, November 13, 2007 2:24 AM To: Discussion list for GROMACS users Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains Hi all, Is it feasible to do parallel tempering (replica exchange) as a function of distance with umbrella sampling applied? I can do REMD for a system containing 2 peptide chains as a function as temperatures, where I grompp each of the systems at different temperatures, and then gather the fullmd.tpr files in one folder with the script I want for full md run. But what if I want to do REMD as a function of distances (for example at 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file), at a fixed temperature, with umbrella sampling applied? If this can be done, how should I write the script for the full md run so that each of the pull.ppa files can recognise the system that it suppose to pull? If anyone know how this can be done? Many thanks. -- Best regards, Huey Ling
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