On 2/05/2012 5:37 PM, Mark Abraham wrote:
On 2/05/2012 5:12 PM, Anik Sen wrote:
Hi,
Am Anik Sen, using gromacs 3.3.2 version. I have a very simple
question to ask,
In the mdp file, like the emmod.mdp or run.mdp needed for a MD run
there are three factors namely,rlist, rcoulomb and rvdw.
1. Is there any minimum value for these three below which the results
will be absurd for any system, or we can use any value for these?
2. For a system we are using 0.1. Is this a right one or not?
You should be attempting to replicate either the parameter regime
under which your force field was developed, or a similar set under
which it has been shown to produce results that agree with real
observations. Pulling numbers out of the air is not appropriate.
And since this is apparently new work, you should upgrade to a more
modern GROMACS for much better performance, more useful resources and
hopefully fewer bugs!
Mark
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