Justn, >Then there are force fields that do better than others, but >the choice must be yours based on a thorough review of available >literature;
Can you provide a list of FFs more suitable for folding and IDP simulations? Thank you, Dmytro ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Monday, November 19, 2018 5:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Best force Field for Protein On 11/18/18 10:46 AM, Edjan Silva wrote: > Dear Gromacs users, I will perform a simulation of a protein with explicit > solvent to verify structural changes in temperatures of 300 k and 310 k. I doubt any force field will give you any meaningful differences at such a small temperature interval. > Given the various force fields available on the gromacs platform, which one > would be most appropriate for my experiment? There's no real way to know. Different force fields do well at different things. Simulating "a protein" can mean a lot of different things. Are you simulating a well-folded protein with a stable tertiary structure? If so, just about any modern force field will perform equivalently. Are you trying to fold a protein or simulate something intrinsically disordered? Then there are force fields that do better than others, but the choice must be yours based on a thorough review of available literature; it's not something that strangers on an Internet forum can conclude for you :) -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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. -- 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.