Which parameter is supposed to be changed to get the sufficient minimized system? Would anyone guide me please?
Thanks in advance Cheers, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, July 25, 2012 4:37 PM Subject: Re: [gmx-users] adding a new atom type On 7/25/12 7:58 AM, Shima Arasteh wrote: > > > Some time ago I defined a new residue and after running grompp I got an >error as there are some interactions assigned multiple times. Then I decided >to duplicate the atoms involved in that residue to avoid this error. That error usually indicates your system is crashing and the DD algorithm is failing. That means either the coordinates are insufficiently minimized, the topology is incorrect, or the .mdp settings are leading to instability. > Next I renamed the atomtypes in atometypes.atp as below: > ZC 12.01100 ; carbonyl C, peptide backbone > ZCT1 12.01100 ; aliphatic sp3 C for CH > ZCT3 12.01100 ; aliphatic sp3 C for CH3 > ZO 15.99900 ; carbonyl oxygen > ZHC 1.00800 ; N-ter H > ZNH1 14.00700 ; peptide nitrogen > ZH 1.00800 ; polar H > ZHB 1.00800 ; backbone H > ZHA 1.00800 ; nonpolar H > > Then I wanted to modify the .itp file, got in to the trouble; I couldn't find > the C atomtype in nonbonded.itp file. Actually I don't know what to do now! > Start over with a fresh set of force field files that you haven't experimented with and troubleshoot the stability of your system. If you Google or search the mailing list archive for this error, tons of useful results show up. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
