[gmx-users] Free energy calculations and speed problems

[David Mobley]

Justin and Michael,

Just to clarify here, I don't think you want the "long cutoff in
vacuum" scheme to give you the same results as the "PME in vacuum"
scheme. That is, if you use PME in vacuum with a periodic box, you
will be including copies of the long-range unscreened electrostatic
interactions between your molecule and its periodic copies. Unless
your box is gigantic, you will probably see significant contributions
to the energy from these. I think for most ordinary vacuum
calculations (i.e. comparing to a vacuum reference state for, say,
hydration free energies) you don't want these contributions and your
desired reference state is something more like the molecule in vacuum,
with no cutoffs, but with no periodic copies. You can achieve that
most easily by simply running in vacuum without pme but making the
cutoffs huge enough to include all of the intramolecular interactions.
Of course, for a protein this would probably be a bad idea for speed
reasons, but for small molecules it can work well.

David


On Tue, May 20, 2008 at 8:06 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> Just to follow up - the cutoff scheme worked quite well.  It gave me energies
> that were ~1% different from those of the PME calculation, which I think
> compares quite well.  The 10-ps run I attempted now takes 3 seconds, instead of
> 20 minutes.
>
> Thanks to everyone for the suggestions.
>
> -Justin
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>> Thanks to everyone for the insights.  I'll try running things with the cutoff
>> and see how it goes.
>>
>> -Justin
>>
>> Quoting Michael Shirts <mrshirts at gmail.com>:
>>
>> > Hi, Justin-
>> >
>> > Have you considered -not- running PME in vacuo?  If you set your
>> > cutoffs and rlist large enough, then you can just run with simple
>> > cutoffs, and it should run -faaaast-.  Of course, you should compare
>> > to the energy with PME -- if they are not equivalent, then you many
>> > need to go back and check your PME parameters for accuracy.
>> >
>> > Best,
>> > Michael
>> >
>> > > I'm running some free energy calculations (in vacuo and in solution) for
>> a
>> > set
>> > > of molecules I am trying to parameterize.  All the molecules are fairly
>> > small,
>> > > about 30-35 atoms in each.  The solvated calculations go smoothly, and
>> > rather
>> > > quickly (~5 hr/ns on two nodes).  I am running into a problem when I do
>> the
>> > in
>> > > vacuo calculations.  Since I am constraining all bonds, I am running
>> things
>> > on
>> > > a local machine in the lab (single core AMD64 Opteron).  I get as far as
>> > NVT
>> > > equilibration (removing charges only) before I give up and kill it, since
>> > it
>> > > takes so long.  A 10-ps NVT run takes about 20 minutes, but that adds up
>> to
>> > > over 5 days for my 5-ns production run!  The machine is no slouch; I have
>> > used
>> > > it to run other small NVT/NPT/MD runs with good performance.  I get
>> similar
>> > > performance on another machine that is even faster (a single CPU of the
>> > 2-CPU
>> > > node on our supercomputer).  The installations of Gromacs on both are
>> fine,
>> > as
>> > > far as I can tell, and both have been used extensively.
>> > >
>> > > I am using Gromacs version 3.3.3, and I have attached my .mdp file and
>> the
>> > tail
>> > > end of my log file for reference.  If anyone notices anything obvious
>> that
>> > I'm
>> > > doing wrong, I would be grateful if you pointed it out!  I see in the log
>> > of
>> > > the slow run (in vacuo) that the 3D-FFT calculation is dominating the CPU
>> > > usage.  Is that indicative of any problem?
>> > >
>> > > Thanks for your attention.
>> > _______________________________________________
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>>
>>
>>
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
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>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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