[gmx-users] Checkpoint files not being written

[Berk Hess]

Hi,

I guess you have nstlist=0.
Try the fix below.

Berk


diff --git a/src/kernel/md.c b/src/kernel/md.c
index dd92d51..225a4bb 100644
--- a/src/kernel/md.c
+++ b/src/kernel/md.c
@@ -1859,7 +1859,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
          * or at the last step (but not when we do not want confout),
          * but never at the first step or with rerun.
          */
-        bCPT = (((gs.set[eglsCHKPT] && bNS) ||
+        bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
                  (bLastStep && (Flags & MD_CONFOUT))) &&
                 step > ir->init_step && !bRerunMD);
         if (bCPT)

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Checkpoint files not being written
Date: Fri, 10 Sep 2010 17:58:33 +0200








Hi,

Do you have no cut-off's and nstlist set to 0?
That's the only case where I could see that checkpoints are missing.
If that's the case, please file a bugzilla so we don't forget to fix this for 4.5.2.

PS -cpnum has nothing to do with this.
I guess it's the bCPT = assignment in md.c that only gets set at NS steps or the last step.

Berk

> Date: Fri, 10 Sep 2010 11:08:26 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Checkpoint files not being written
> 
> 
> Hi All,
> 
> I don't know if this is a new (intended) feature or a bug, so I figured I'd ask 
> :)  I'm running version 4.5.1 to do some implicit solvent simulations.  What 
> I've noticed is that, no matter how long the simulation runs, I only ever get a 
> checkpoint file at the end of the simulation, and thus the checkpoint interval 
> (which I have left at the default value of 15) is ignored.  All the simulations 
> I've done are sufficiently long (at least one hour) such that they should have 
> produced checkpoint files according to this interval.
> 
> Could this issue be related to the introduction of the -cpnum flag, which is set 
> to "no" by default?  I've poked around a bit in the mdrun code, but I easily 
> lose my place trying to trace what's going on.  I've tried specifically adding 
> -cpnum to my mdrun command line, but still I am not receiving any intermediate 
> checkpoint files at the requested -cpt interval.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at 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 at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 		 	   		  

-- 
gmx-users mailing list    gmx-users at 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 at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100910/8b7f9369/attachment.html>