As I explained here before, I get an error ( some interactions seem to be assigned multiple times). I suspected the top file, so checked it and visualized the output of em.mdp; the output seems to be correct and I don't see any bonds behaves strangely. As I studied in mailing lists it and you also mentioned , this may happen because of the insufficient minimization. I'm wondering how a good and sufficient minimization is provided?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, July 27, 2012 10:51 PM Subject: Re: [gmx-users] adding a new atom type On 7/27/12 1:08 PM, Shima Arasteh wrote: > > > Which parameter is supposed to be changed to get the sufficient minimized > system? Would anyone guide me please? > This question is very vague. In principle, any system can be minimized but the definition of "sufficient" depends on your goals. -Justin > 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 > -- ======================================== 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
