Thanks Tom, It may easily be that the 6- bond type works in mdrun but not in mdrun-openmm. This would be an explanation for the ridiculous force constants
Hans Am Mittwoch, den 06.01.2010, 23:15 +0000 schrieb TJ Piggot: > Please keep all correspondence on the GROMACS mailing list, it gives you a > much greater chance of someone being able to help you. > > I have used this bond type before and have had no problems (with force > constants much smaller than those which you apply). I would make sure that > your box is big enough so that this bond is not being applied across the > boundary. Otherwise someone else may have more ideas to help you. > > Tom > > ------------ Forwarded Message ------------ > Date: Wednesday, January 06, 2010 22:43:20 +0100 > From: Hans HEINDL <hhei...@terra.es> > To: TJ Piggot <t.pig...@bristol.ac.uk> > Cc: > Subject: simulationg a distance restraint with a type 6 bond in gromacs > > Hi, > > As you remember we discussed simulation of a restraint which is not yet > implemented in mdrun-openmm by creating a 'bond'. Type 1 bonds did not > work but the type 6 did the job but I could not restrain the distance at > the value I projected. The distance between the ends of my peptide > should remain 57 angstroms and the best I accomplished was holding the > distance fairly well for a ns and then it broke down to a much smaller > value. (I tried to define the bond with: > > 1 614 6 5.761 400000 > > with the energy term for the bond length obviously too small. But even > if I got up to 300 000 000 up to 1 000 000 000 I got no proper result. > > The best results were recieved with > > 1 614 5 5.671 5.671 5.671 5.671 > > but even with such an extreme example the distance tended to shrink > > > kind regards > > Hans HEINDL > University of Westminster UK > > > > ---------- End Forwarded Message ---------- > > > > ---------------------- > TJ Piggot > t.pig...@bristol.ac.uk > University of Bristol, UK. > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
