[gmx-users] Re: Distance restraints not working

[tdgrant1]

There are a few possibilities. 
> 
> 1. Numbering in [distance_restraints] is not based on .gro numbering.  The
> atom 
> 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
> default. 
> Check the mdout.mdp file or your .tpr file to ensure that you have a
> sensible 
> 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
typo.

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?

-Tom

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