<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<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>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<span id="OLK_SRC_BODY_SECTION" 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">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>> on behalf of Igor Leontyev <<a href="mailto:ileontyev@ucdavis.edu">ileontyev@ucdavis.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a 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 href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>" <<a 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>
</div>
<div><br>
</div>
<div><style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div dir="ltr">
<div id="divtagdefaultwrapper" 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>
<p></p>
</div>
</div>
</div>
</span>
</body>
</html>