I want to use it to energy minimise a system that has severe clashes. The EM always crashes, even if I reduce the step-size. It could also be useful for NMR refinement to allow atoms to move through each other in order to satisfy distance restraints.
Andreas ________________________________________ From: [email protected] [[email protected]] On Behalf Of Vitaly Chaban [[email protected]] Sent: 01 June 2011 20:30 To: [email protected] Cc: [email protected] Subject: Re: [gmx-users] Re: scaling non-bonded interactions Doesn't increased temperature work for this purpose? On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <[email protected]> wrote: > > > Vitaly Chaban wrote: >>> >>> Is it possible to globally scale all non-bonded interactions by a factor >>> ? I know there are energy exclusion groups, but that is an all or nothing >>> approach, while I would like to reduce non-bonded interaction potentials to >>> e.g. 10% of their normal value. >>> >>> If this is not possible, I suggest to have this as an option in the >>> mdp-file. >> >> >> I don't see much sense in such uniform scaling. >> >> > > Such scaling can be useful for overcoming energy barriers and speeding up > equilibration. This function is hinted at in the description of the > couple-moltype .mdp keyword. I don't know if that's the intent here, but it > certainly does have an application. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
