[gmx-users] Checkpoint files not being written
gmx3 at hotmail.com
Fri Sep 10 18:03:56 CEST 2010
I guess you have nstlist=0.
Try the fix below.
diff --git a/src/kernel/md.c b/src/kernel/md.c
index dd92d51..225a4bb 100644
@@ -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);
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
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.
> 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 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
> gmx-users mailing list gmx-users at gromacs.org
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