[gmx-users] Re: Distance restraints not working
tgrant at hwi.buffalo.edu
Wed May 23 20:26:57 CEST 2012
There are a few possibilities.
> 1. Numbering in [distance_restraints] is not based on .gro numbering. The
> numbers supplied are only relevant within the [moleculetype] to which they
> belong, much like [position_restraints]. Also make sure that the
> [distance_restraints] block is in the correct location in the topology.
> 2. You've omitted the dihre_fc keyword, though it is set to 1000 by
> Check the mdout.mdp file or your .tpr file to ensure that you have a
> value here. Setting values of fac that high are unnecessary.
Thanks for your help. I have it working now. It actually turned out to be a
I have an unrelated question though. After running the temperature and
pressure equilibration, grompp tells me my md run will produce ~150 GB of
data. I'd really like to avoid such an enormous amount of data. The system
is ~300,000 atoms and I will be running 20 ns of simulation (~3 days on our
cluster according to the equilibration output). Can I simply change the
output control from saving the various files at every 2 ps to every, say, 20
ps? I realize it's a large jump compared to 2 ps, but 150 GB is a lot of
data. Will changing the output control so drastically adversely affect the
simulation in any way?
View this message in context: http://gromacs.5086.n6.nabble.com/Distance-restraints-not-working-tp4997654p4997692.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
More information about the gromacs.org_gmx-users