<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>Gromacs uses a more complicated, but also more efficient way to<br>determine the virial.<br>If you write your own program, I would the much simpler direct way<br>of just calculating r x f in all the force loops.<br>Gromacs 4.0 still always uses shift vectors, but in parallel the graph is not used.<br><br>Berk<br><br>> Date: Fri, 28 Nov 2008 15:32:55 +0800<br>> From: xuji@home.ipe.ac.cn<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] How to calculate virial in gromacs-4.0?<br>> <br>> Hi all<br>> <br>> I want to do pressure coupling in my own program.<br>> So These days I read associated codes in Gromacs_4.0 and I find that it<br>> must sum the virial first. In Gromacs-3.3.3 you use the intramolecular shift(graph)<br>> to sum the virial of the covalent bonds, but in Gromacs-4.0 the graph variable seems to be NULL<br>> when run the mdrun with domain decomposition. Is it the true? <br>> And if it's true how do you sum the
virial with the periodic boundary condition <br>> in Gromacs_4.0 with domain decomposition? Can someone explain the way of summing <br>> virial in Gromacs_4.0 in detail? Or can you recommend some resoures about summing the virial with <br>> the periodic boundary condition? <br>> <br>> Appreciate any help in advance!<br>> <br>> Best<br>> wishes!<br>> <br>> <br>> xuji<br>> xuji@home.ipe.ac.cn<br>> 2008-11-28<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>