<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
Hi,<br><br>I guess you have nstlist=0.<br>Try the fix below.<br><br>Berk<br><br><br>diff --git a/src/kernel/md.c b/src/kernel/md.c<br>index dd92d51..225a4bb 100644<br>--- a/src/kernel/md.c<br>+++ b/src/kernel/md.c<br>@@ -1859,7 +1859,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],<br> * or at the last step (but not when we do not want confout),<br> * but never at the first step or with rerun.<br> */<br>- bCPT = (((gs.set[eglsCHKPT] && bNS) ||<br>+ bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||<br> (bLastStep && (Flags & MD_CONFOUT))) &&<br> step > ir->init_step && !bRerunMD);<br> if (bCPT)<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Checkpoint files not being written<br>Date: Fri, 10 Sep 2010 17:58:33 +0200<br><br>
<meta http-equiv="Content-Type" content="text/html; charset=unicode">
<meta name="Generator" content="Microsoft SafeHTML">
<style>
.ExternalClass .ecxhmmessage P
{padding:0px;}
.ExternalClass body.ecxhmmessage
{font-size:10pt;font-family:Tahoma;}
</style>
Hi,<br><br>Do you have no cut-off's and nstlist set to 0?<br>That's the only case where I could see that checkpoints are missing.<br>If that's the case, please file a bugzilla so we don't forget to fix this for 4.5.2.<br><br>PS -cpnum has nothing to do with this.<br>I guess it's the bCPT = assignment in md.c that only gets set at NS steps or the last step.<br><br>Berk<br><br>> Date: Fri, 10 Sep 2010 11:08:26 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Checkpoint files not being written<br>> <br>> <br>> Hi All,<br>> <br>> I don't know if this is a new (intended) feature or a bug, so I figured I'd ask <br>> :) I'm running version 4.5.1 to do some implicit solvent simulations. What <br>> I've noticed is that, no matter how long the simulation runs, I only ever get a <br>> checkpoint file at the end of the simulation, and thus the checkpoint interval <br>> (which I have left at the default value of 15) is ignored. All the simulations <br>> I've done are sufficiently long (at least one hour) such that they should have <br>> produced checkpoint files according to this interval.<br>> <br>> Could this issue be related to the introduction of the -cpnum flag, which is set <br>> to "no" by default? I've poked around a bit in the mdrun code, but I easily <br>> lose my place trying to trace what's going on. I've tried specifically adding <br>> -cpnum to my mdrun command line, but still I am not receiving any intermediate <br>> checkpoint files at the requested -cpt interval.<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>                                           
<br>--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists                                            </body>
</html>