From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Oct 23 2006 - 14:45:27 CDT
Protein RMSD is another observable that can be used to judge.
There is a script in the VMD tutorial that can easily be modified for
your protein: http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-
If the RMSD becomes more or less level (stops growing), then it is
On Oct 23, 2006, at 2:06 PM, Mark Abraham wrote:
> tamal_at_iitk.ac.in wrote:
>> Before my Production run in NPT simulation for a PBC condition, i
>> am doing
>> my NVT simulation for equilibriation.What i observe is that for 1
>> ns NVT
>> run, the Potential Energy gets stabilized at -9000 kcal/mol,
>> whereas the
>> final energy during heating stage is somewhat less (-9600 kcal/mol).
>> Can i concude that equilibriation has reached ?
> The value and its relative magnitude don't have any particular
> meaning - they just suggest that the equilibrated value under the
> two prevailing schemes is different. Equilibration is achieved if
> various observables have converged - potential energy is one of them.
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