Hello, Is it correct for you that in your topolgy file, some atoms have wrong mass (i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN molecule ? Are they at the end ?
Stephane ------------------------------ Message: 3 Date: Thu, 7 Feb 2013 19:13:11 +0330 From: Ali Alizadeh <[email protected]> Subject: [gmx-users] Re:united atom To: gmx-users <[email protected]> Message-ID: <capfuhmvnbu3v0verko_faxuvkk0qtg7hgazatjp16-a1rsh...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Justin Thank you for your reply, I want to use Nose-Hoover thermostat and MTTK barostat and shake algorithm and md-vv integrator, but I got this error: ----------------------------------- Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -------------------------------------- A part of my topology file: ------------------ [ moleculetype ] ; Name nrexcl DECANE 9 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 LI rtp LI q 0.0 1 opls_071 0 LI C1 1 0 14.027 ; qtot 0 2 opls_071 0 LI C2 2 0 14.027 ; qtot 0 3 opls_071 0 LI C3 3 0 14.027 ; qtot 0 4 opls_071 0 LI C4 4 0 14.027 ; qtot 0 5 opls_071 0 LI C5 5 0 14.027 ; qtot 0 6 opls_071 0 LI C6 6 0 14.027 ; qtot 0 7 opls_068 0 LI C7 7 0 15.035 ; qtot 0 8 opls_071 0 LI C8 8 0 14.027 ; qtot 0 9 opls_068 0 LI C9 9 0 15.035 ; qtot 0 10 opls_071 0 LI C10 10 0 14.027 ; qtot 0 ------------------------------- On 2/7/13 9:46 AM, Ali Alizadeh wrote: > Dear All user > > There are 350 decane molecules in my simulation box, > > I like doing a simulation(npt ensemble) by a united atom force field, > Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in > gromacs? > > Beside, How can I neglect coloumb interaction(non-bonded) and > dihedrals(bonded)? > >>The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA >>(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly >>ancient force field. In that case, there are no Coulombic interactions >>anyway, >>because the united-atom carbons should not have any charge. If you want to >>neglect dihedrals, I think you're hacking the force field in a way that makes >>no >>sense. >>-Justin -- Sincerely Ali Alizadeh University of Tehran College of engineering(Fanni) Department of chemical engineering IPE (Institute of Petroleum Engineering) M.Sc Candidate, class of 2013 B.Sc Graduate 2011(University of Tehran,Fanni) -- 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
