AMBER Archive (2007)

Subject: Re: AMBER: equilibration in explicit solvent

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Thu Feb 08 2007 - 11:37:39 CST

I have a strange problem with sander minimization which I have never had
before. I am trying to run an NVT equilibration of a solute in explicit
solvent. I have two distinct conformations of the solute and want to see
what happens to each of them when equilibrating each separately in
explicit solvent.

I originally had the problem that I had a different number of water
molecules when specifying a solvent box of the same volume for each
conformation. With Ilyas Yildirim's help, I managed to ensure I have the
same number of water molecules in each case. Ilyas' script is quite smart
and better than manually removing extra waters -- it removes waters from
the outer layers of the box.

However, now I have a strange thing that sander hangs when I start the
equilibration with the solute fixed. On the conformation for which I did
not remove waters, sander is fine - it runs with no problems and I can see
the progress in mdinfo. But for the case where I removed the extra waters,
no mdinfo file gets written out, and the .out file is empty. I see no sign
of progress at all, even though the equilibration scripts in each case are
exactly the same.

Here is the script I am using to keep the solute fixed first:
----------------------------------------------------------------
echo "STAGE1: HOLDING THE PROTEIN FIXED AND MINIMIZING SOLVENT"
cat <<eof > mdin
  initial minimisation solvent
  &cntrl
    imin=1,
    maxcyc=5000,
    ncyc=500,
    ntb=1,
    ntr=1,
    cut=10,
  &end
Hold the PROTEIN fixed
500.0
RES 1 18
END
END
eof
sander -O -i mdin -o frame_wat_min1.out -p frame_wat.top -c
frame_wat.inpcrd -r
frame_wat_min1.rst -ref frame_wat.inpcrd
-----------------------------------------------------------------

If anybody has any insight, I would greatly appreciate any pointers. I am
not sure what is going on.

-Amarda
***********************************
Amarda Shehu,
Graduate Student, Computer Science,
Rice University.
***********************************

On Sun, 4 Feb 2007, David A. Case wrote:

> On Sun, Feb 04, 2007, Amarda Shehu wrote:
>>
>> These two conformations have been obtained with a newly developed method
>> in implicit solvent (using ff03 and GB). I am preparing a manuscript for
>> publication, but my advisor has asked me to make sure that in explicit
>> solvent, these conformations retain both their structural integrity and
>> their energetic difference.
>
> Even if you did everything you originally suggested, you would only get the
> *potential* energy difference between the two solvated systems. But the
> implicit solvent calculation estimates the *free* energy of the solvent.
> The difference is the entropy effect, mentioned by Prof. Duan.
>
> Testing the structural integrity is straightforward, and it sounds like you
> have already done that. Getting a comparable energetic number is more
> involved. It sounds like you probably want to think about a thermodynamic
> integration calculation to compute the free energy difference between the two
> solutes.
>
> ....good luck...dac
>
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