Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX

From: David A Case <david.case.rutgers.edu>
Date: Wed, 18 Nov 2015 09:22:17 -0500

On Wed, Nov 18, 2015, V. Kumar wrote:
>
> I am trying to perform simulated annealing in WATER.(TIP3PBOX) in the
> presence of NMR restraints. When I solvated my peptide in a TIP3PBOX 10A,
> leap added 10000 water molecules.
> Because of that my simulation is running slow.

There's not an easy way around this. You already have a minimal (or even less
than minimal) buffer (10 Ang.). Use solvateOct rather than solvateBox (if you
have not already done this.)

Generally, NMR refinement in explicit solvent is done at the final stages of
refinement, so you can hope to already have a "pretty good" (tm) structure.
Be careful about how high an annealing temperature you use with explicit
solvent.

It is possible that the poor performance you report is caused by a poor choice
of input parameters: be sure to compare what you are doing to examples
in the tutorials (doesn't have to be simulated annealing).

...dac


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Received on Wed Nov 18 2015 - 06:30:06 PST
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