<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="EC_stopSpelling">From: gmx3@hotmail.com<br>To: lastexile7gr@yahoo.de<br>Subject: RE: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs<br>Date: Fri, 4 Jul 2008 10:14:14 +0200<br><br>
<meta http-equiv="Content-Type" content="text/html; charset=unicode">
<meta name="Generator" content="Microsoft SafeHTML">
<style>
.ExternalClass .EC_hmmessage P
{padding:0px;}
.ExternalClass body.EC_hmmessage
{font-size:10pt;font-family:Tahoma;}
</style>
<div style="text-align: left;">Hi,<br><br>It is completely clear to me if your 1-4 and 1-5 interactions use the same potential types and cut-off's.<br>If they do, you can do it with the user tables.<br>Set nrexcl in the topology to 4.<br>I think you will then have add the 1-5 interactions manually to the [ pairs ] section.<br>mdrun has separate input files for non-bonded and bonded interactions.<br>You will have to fill these tables with the functions with the right cut-offs and<br>switching functions.<br><br>Berk.<br></div><br><br><hr id="EC_EC_stopSpelling">Date: Tue, 1 Jul 2008 14:48:21 +0000<br>From: lastexile7gr@yahoo.de<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit;" valign="top">Hello,<br><br>trying to implement my force field into gromacs I have figured out that it is of vital importance to use diferrent cut-offs among different kind of atoms. <br><br>I have 1-4 and 1-5 interactions with a set of epsilon and sigma parameters and the non bonded interactions (more than 4 bonds appart) with a different set. Every interaction among different type of atoms have different rvdw-switch and rvdw cutoffs.<br><br>As a result I have to use a tabulated potential both for 1-4 and 1-5 interactions AND non-bonded interactions (1-6 and above). My question is how is it possible someone to do that in gromacs. How gromacs would be able to discern whether the interaction is 3 or 4 bonds appart OR more than 4 bonds?<br><br>In case I cannot use tabulated potential for the interactions I'm
interested in, could I keep the pair interactions as they are up to now
under the pairs section and use at least tabulated potential for the
non-bonded interactions?<br><br>In any case of the above what would be the meaning of rvdw-switch and rvdw cutoffs in the mdp file?<br><br>The number of different interactions I have are 6. Is it possible while tabulating the non-bonded interactions to have both energy and pressure correction? <br><br>I have also seen that I can use reduced parameters (eplsilon and sigma) for all the non-bonded interactions, yet (correct me if I'm wrong) I do not think that this solves the problem of different cutoffs. That way only one interaction would have the correct cutoff.<br><br>Unfortunately all my efforts up to now with one global cutoff don't bring the anticipated results.<br><br>Thank you in advance,<br>Nikos<br></td></tr></tbody></table><br>
<hr size="1">
Unglücklich mit Ihrer Mail-Adresse?
<br>
Registrieren Sie Ihre Wunschmailadresse@ymail.com
<br>
<a href="http://de.docs.yahoo.com/mail/wunschmailadresse/index.html" target="_blank">
Millionen neuer Mail-Adressen - jetzt bei Yahoo!</a><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a>
<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>