<div dir="ltr">and/or test with an earlier version of the code?<div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Dec 10, 2015 at 6:17 PM Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
<div>On 12/10/2015 07:59 AM, Shirts, Michael
R. (mrs5pt) wrote:<br>
</div>
<blockquote type="cite">
<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>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)"><br>
</span></div>
<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>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">
<br>
</div>
<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>
</blockquote></div><div text="#000000" bgcolor="#FFFFFF">
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 <a href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a> and attach a tpr file
that reproduces the problem?<br>
<br>
Cheers,<br>
<br>
Berk</div><div text="#000000" bgcolor="#FFFFFF"><br>
<blockquote type="cite">
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">
<br>
</div>
<span style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">
<div style="font-family:Calibri;font-size:14pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span><<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank"><a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a></a>>
on behalf of Igor Leontyev <<a href="mailto:ileontyev@ucdavis.edu" target="_blank">ileontyev@ucdavis.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org" target="_blank"><a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a></a>"
<<a href="mailto:gmx-developers@gromacs.org" target="_blank">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 href="mailto:gmx-developers@gromacs.org" target="_blank"><a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a></a>"
<<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
<span style="font-weight:bold">Subject: </span>[gmx-developers]
dEkin/dl parallelization issue<br>
</div>
<div><br>
</div>
<div>
<div dir="ltr">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
</div>
</div>
</div>
</span>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
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