On 9/6/17 5:36 AM, Seera Suryanarayana wrote:
Dear gromacs users, I have gone through one gromacs tutorial of md simulation in solvent. Where they mentioned that successive removal of position restrain. In other words first they have done NPT ensemble with 1000 1000 1000 energy constants, then re executed the NPT ensemble with 100 100 100 energy constants and finally third time they ran the NPT ensemble with 10 10 10 energy constants. After this run they have stated the real MD production run with position restraint. But I have done NPT ensemble only with 1000 1000 1000 force constant and then I removed the complete position restrains before MD production run. My question comes here, Is there any difference between their methodology and my methodology?
Well, naturally there is a difference, but whether or not it matters is a different question :)
I have never done step-wise removal of position restraints. Some people swear by it. Same story with warming a system from 0 K to a target temperature - I see no benefit but others believe it's necessary. The purpose of equilibration is to relax the system and achieve a reasonably stable thermodynamic ensemble. If you've done that, proceed with your simulation.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 [email protected] | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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 [email protected].
