> Hello all, > > I am trying to apply a set of harmonic distance restraints between pairs > of > protein atoms in my system, which is protein/ligand/water/ions in a > periodic box. > > The way i am doing this is to use the bond type 6 and to add these bonds > at > the end of the [bonds] section in my topology file, after the system has > been energy minimised and i have performed position restrained MD, without > these harmonic distance restraints. > > I can then run it through grompp with no problems and start mdrun. If i > only have a few (ie less than about 30) harmonic distance restraints then > the simulation if fine and runs happily. However if i increase the number > of restraints then mdrun crashes due to lincs warnings and it also says > that the are inconsistent shifts, (the number of inconsistent shifts > varies > depending on which atoms i choose to restrain and also the number of atoms > chosen) a warning not seen with less harmonic distance restraints.
Why do you need more harmonic restraints? > I should also say that i have run this system without these harmonic > restraints without problems for tens of nanoseconds already. Also this > problem can be repeated if i try to use the [distance_restraints] however > it requires less restraints to get the inconsistent shift warning (and > lincs problems) this way. > > If anyone can give me an idea of what is causing this problem it would be > warmly appreciated, or even just how to detect which of the harmonic > distance restraints will cause the problem before i run mdrun so i can > replace the problem 'bonds' in the topology file. You can't tell a priori, but if you watch the trajectory you should start to get an idea what is breaking where and this will narrow down the number of inappropriate restraints. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
