<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 25/05/2011 12:50 AM, <a class="moz-txt-link-abbreviated" href="mailto:jen.johnston@lycos.com">jen.johnston@lycos.com</a> wrote:
<blockquote
cite="mid:1740119155.14884.1306248607891.JavaMail.mail@webmail06"
type="cite">Hi,<br>
I have exactly the same problem as is described below. I am using
version 4.5.4 with the Plumed metadynamics plugin.<br>
<br>
I was wondering if there was any update on dealing with the bug?<br>
</blockquote>
<br>
The original poster never filed a bug request, so there was never
anything to debug.<br>
<br>
I can do so if you have a reproducible non-Plumed case where
gmxcheck on the .tpr files (and any .cpt files input with mdrun
-cpi) reveals no differences in things like init_step and nsteps,
and mdrun thinks there is a mismatch. If so, please file a Redmine
request. <a moz-do-not-send="true" class="parsedLink"
href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1740119155.14884.1306248607891.JavaMail.mail@webmail06"
type="cite">Many thanks,<br>
Jen<br>
<br>
Today's Topics:<br>
<div class="replyBody">
<blockquote class="email_quote" style="border-left: 2px solid
rgb(38, 127, 219); margin: 0pt 0pt 0pt 1.8ex; padding-left:
1ex;"><br>
1. Re: Replica Exchange MD using Gromacs (Mark Abraham)<br>
2. Re: FW: protein split over boundary (ravi sharma)<br>
3. Re: FW: protein split over boundary (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 01 Apr 2011 22:30:56 +1100<br>
From: Mark Abraham <<a moz-do-not-send="true"
class="parsedEmail" href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Replica Exchange MD using Gromacs<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" class="parsedEmail"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true" class="parsedEmail"
href="mailto:4D95B770.1070805@anu.edu.au" target="_blank">4D95B770.1070805@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 1/04/2011 6:52 PM, bsmith wrote:<br>
> On 01/04/2011, at 6:29 PM, Mark Abraham wrote:<br>
><br>
>> On 1/04/2011 6:03 PM, Ruchi Gupta wrote:<br>
>>> Dear gmx-users,<br>
>>><br>
>>> I am facing some problems while running replica
exchange MD using <br>
>>> Gromacs.<br>
>>><br>
>>> Few seconds after the job submission it ends with
the following <br>
>>> error message:<br>
>>><br>
>>> "<br>
>>> Initializing Replica Exchange<br>
>>><br>
>>> Repl There are 6 replicas:<br>
>>> Multi-checking the number of atoms ... OK<br>
>>> Multi-checking the integrator ... OK<br>
>>> Multi-checking init_step+nsteps ...<br>
>>> init_step+nsteps is not equal for all subsystems<br>
>>> subsystem 0: 0<br>
>>><br>
>>> subsystem 1: 50000<br>
>>> subsystem 2: 0<br>
>>> subsystem 3: 50000<br>
>>> subsystem 4: 0<br>
>>> subsystem 5: 50000<br>
>>><br>
>>>
-------------------------------------------------------<br>
>>> Program mdrun, VERSION 4.5.4<br>
>>> Source code file: main.c, line: 249<br>
>>><br>
>>><br>
>>> Fatal error:<br>
>>> The 6 subsystems are not compatible<br>
>>><br>
>>> For more information and tips for
troubleshooting, please check the <br>
>>> GROMACS<br>
>>> website at<a moz-do-not-send="true"
class="parsedLink"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
>>><br>
>>>
-------------------------------------------------------<br>
>>><br>
>>> "<br>
>>><br>
>>> I am using a "single .gro file" and "6 different
md.mdp" files (at 6 <br>
>>> different temperatures) for generating "6 .tpr
files", respectively. <br>
>>> But the simulation doesn't work.<br>
>>><br>
>>><br>
>>> I have compared the ".tpr files" using "gmxdump"
and "gmxcheck" <br>
>>> Gromacs commands and they seem fine with respect
to nsteps and <br>
>>> init_step information.<br>
>><br>
>> So, to be clear, gmxcheck says that for no pair of
.tprs does <br>
>> init_step or nsteps differ...<br>
>><br>
>> What is your mdrun command line? Are you using
checkpoint files?<br>
>><br>
>> Mark<br>
>> -- <br>
>> gmx-users mailing list <a moz-do-not-send="true"
class="parsedEmail" href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a> <br>
>> <<a moz-do-not-send="true" class="parsedLink"
href="mailto:gmx-users@gromacs.org" target="_blank">mailto:gmx-users@gromacs.org</a>><br>
>> <a moz-do-not-send="true" class="parsedLink"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <br>
>> <a moz-do-not-send="true" class="parsedLink"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
>> Please don't post (un)subscribe requests to the list.
Use the www <br>
>> interface or send it to <a moz-do-not-send="true"
class="parsedEmail"
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a moz-do-not-send="true"
class="parsedLink"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
> 1) Comparison of the .tpr files using gmxdump reveals no
differences <br>
> but for the temperatures and the velocities in each i.e.
init_step and <br>
> nsteps have the same values (0 and 50000, respectively)
in all files.<br>
><br>
> 2) We have tried running mdrun without checkpointing
(-cpt -1) and <br>
> with checkpointing with no change in the outcome.<br>
<br>
That sounds like a bug. Please create a new Redmine issue here
<br>
<a moz-do-not-send="true" class="parsedLink"
href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a>
and attach your .tpr and .mdp files - <br>
preferably in a compressed archive file. You should get the
option to <br>
assign it to me - please do.<br>
<br>
Mark<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true" class="parsedLink"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110401/471a7c08/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110401/471a7c08/attachment-0001.html</a><br>
<br>
<br>
</blockquote>
</div>
</blockquote>
<br>
</body>
</html>