Hi, If you are using PBC, mdrun will sometimes write sets of coordinates such that molecules appear "broken" across periodic boundaries. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for solution approaches.
Linear species can sometimes have other problems, which have been discussed on the mailing list before. Mark ----- Original Message ----- From: [email protected] Date: Monday, September 6, 2010 18:43 Subject: [gmx-users] the broken of the molecules To: gmx-users <[email protected]> > Hello, I do the energy minimization of the butylene box , but some butylene > molecules are broken after that. The butylene itp file is produced by PRODRG, > as follows: > > [ moleculetype ] > ; Name nrexcl > BUT 3 > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 CH3 1 BUT C9 1 0.0049 15.0350 > 2 CH2 1 BUT C6 1 -0.02442 14.0270 > 3 C 1 BUT C3 1 0.07957 13.0190 > 4 C 1 BUT C2 1 -0.06005 14.0270 > [ bonds ] > ; ai aj fu c0, c1, ... > 2 1 2 0.155 7150000.0 0.155 7150000.0 ; C6 C9 > 2 3 2 0.153 7150000.0 0.153 7150000.0 ; C6 C3 > 3 4 2 0.135 7150000.0 0.135 7150000.0 ; C3 C2 > [ pairs ] > ; ai aj fu c0, c1, ... > 1 4 1 ; C9 C2 > [ angles ] > ; ai aj ak fu c0, c1, ... > 1 2 3 2 112.5 520.0 112.5 520.0 ; C9 C6 C3 > > 2 3 4 2 125.0 610.0 125.0 610.0 ; C6 C3 C2 > > [ dihedrals ] > ; ai aj ak al fu c0, c1, m, ... > 1 2 3 4 1 0.0 1.0 6 0.0 1.0 6 ; dih C9 C6 > C3 C2 > > Can you show me why the butylene molecules would be broken? > Thank you very much ! > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
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