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<div class="moz-cite-prefix">On 12/10/2015 07:59 AM, Shirts, Michael
R. (mrs5pt) wrote:<br>
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cite="mid:D28E701E.8C007%25mrs5pt@eservices.virginia.edu"
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<div><font face="Calibri,sans-serif">> </font><span
style="background-color: rgb(255, 255, 255);"><font
face="Calibri,Arial,Helvetica,sans-serif"><span
style="font-size: 16px;">The work around is do not include
fep-lambdas or mass-lambdas specification in mdp-file.</span></font></span></div>
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<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Or explicitly setting the masses to be the same. In virtually
all cases of interest, there's a cancellation of the kinetic
energy term (one is interested in solvent alchemical change -
ideal gas change or solvent alchemical change - protein complex
alchemical change).</div>
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<br>
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<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
I mean, the error shouldn't be there, but it's a very easy error
to work around.</div>
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This contribution also converges very quickly to its equilibrium
value which is trivial to calculate.<br>
<br>
But I don't see any obvious bug in the code (but it's quite
complex). Does this happen with MPI and/or thread parallelization?<br>
Could you file an issue redmine.gromacs.org and attach a tpr file
that reproduces the problem?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<blockquote
cite="mid:D28E701E.8C007%25mrs5pt@eservices.virginia.edu"
type="cite">
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<span style="font-weight:bold">From: </span><<a
moz-do-not-send="true"
href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a></a>>
on behalf of Igor Leontyev <<a moz-do-not-send="true"
href="mailto:ileontyev@ucdavis.edu">ileontyev@ucdavis.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a
moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org"><a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a></a>"
<<a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday,
December 9, 2015 at 8:24 PM<br>
<span style="font-weight:bold">To: </span>"<a
moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org"><a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a></a>"
<<a moz-do-not-send="true"
href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Subject: </span>[gmx-developers]
dEkin/dl parallelization issue<br>
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<p>Hi.<br>
It looks there is a parallelization bug in computation
of "dEkin/dl" term in free energy simulations.<br>
I simulate ddG with gromacs 5.1 and mixed topology, i.e.
need dG in protein and in water:<br>
ddG = dG(InProtein) - dG(InWater)<br>
The alchemical transformation involves only one atom
mutation H->Cl. I expect that dEkin/dl terms
InProtein and InWater cancel each other. But it is not
always true.<br>
</p>
<p>In 1 or 2 core simulations I get <dEkin/dl >
value about 130 kJ/mol, for 4 and 8 cores <dEkin/dl
> drops down to ~ 65 kJ/mol and for 16 cores it drops
down again about twice.<br>
</p>
<br>
<br>
<br>
Igor<br>
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