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On 19/10/2011 5:25 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:CAKVtM2sE7DYbaUukqxAVWU4m79-5-Y8_Vvj6b95uGP0RO8WnKQ@mail.gmail.com"
type="cite">Thanks for your reply<br>
I dont understand "step number is at least as large as nstlist".
can you some explain?<br>
</blockquote>
<br>
The first output you cite was written at step 100, of the 15M you
asked for. nstlist is in your .mdp file. All this stuff really
doesn't matter at all.<br>
<br>
<blockquote
cite="mid:CAKVtM2sE7DYbaUukqxAVWU4m79-5-Y8_Vvj6b95uGP0RO8WnKQ@mail.gmail.com"
type="cite">Furthermore, if the file system doesnt write the
buffer to the destination screen/file, then does that mean <span
id="result_box" class="short_text" lang="en"><span class="hps">there
is a problem? </span></span>for example<br>
if it shows as the following:<br>
15000000 steps, 30000.0 ps.<br>
</blockquote>
<br>
Not really. There's just some latency between the program writing
the output and you being able to read it. If the program is allowed
to exit normally, then all the buffers will be flushed eventually.
Details vary from case to case and depend on your hardware and OS.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKVtM2sE7DYbaUukqxAVWU4m79-5-Y8_Vvj6b95uGP0RO8WnKQ@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">2011/10/19 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 19/10/2011 5:04 PM, ahmet yıldırım
wrote:
<blockquote type="cite">For example;<br>
<br>
grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o
run.tpr<br>
mdrun -v -deffnm run<br>
<br>
...<br>
15000000 steps, 30000.0 ps.<br>
step 100, will finish Sun Nov 27 19:11:00 2011<br>
<br>
Sometimes it shows as the following:<br>
15000000 steps, 30000.0 ps.<br>
That is, there is not "will finish Sun Nov 27 19:11:00
2011" sentence <br>
</blockquote>
<br>
</div>
It only writes it when certain conditions are true (e.g.
step number is at least as large as nstlist), and it only
appears when the file system decides to write the buffer to
the destination screen/file.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">2011/10/19 Emanuel Birru <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Emanuel.Birru@monash.edu"
target="_blank">Emanuel.Birru@monash.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">You
can get them in the log file. (At the bottom)<br>
<br>
Cheers,<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
=========================================================<br>
Emanuel Birru<br>
PhD Candidate<br>
<br>
Faculty of Pharmacy and Pharmaceutical Sciences<br>
Monash University (Parkville Campus)<br>
381 Royal Parade, Parkville<br>
Victoria 3052, Australia<br>
<br>
Tel: Int <a moz-do-not-send="true"
href="tel:%2B%2061%203%209903%209187"
value="+61399039187" target="_blank">+ 61 3 9903
9187</a><br>
E-mail: <a moz-do-not-send="true"
href="mailto:emanuel.birru@monash.edu"
target="_blank">emanuel.birru@monash.edu</a><br>
<a moz-do-not-send="true"
href="http://www.pharm.monash.edu.au"
target="_blank">www.pharm.monash.edu.au</a><br>
<div><br>
-----Original Message-----<br>
From: <a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>]
On Behalf Of Mark Abraham<br>
Sent: Wednesday, 19 October 2011 3:08 PM<br>
To: Discussion list for GROMACS users<br>
Subject: Re: [gmx-users] calculation time<br>
<br>
On 19/10/2011 5:26 AM, ahmet yıldırım wrote:<br>
</div>
<div>> Dear users,<br>
><br>
> Sometimes, in the end ( in production
simulation), Gromacs doesn't<br>
> show calculation/finish time on screen,
why? How can we show it?<br>
<br>
</div>
<div>
<div>I don't know what you mean.<br>
<br>
Mark<br>
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<br>
-- <br>
Ahmet YILDIRIM<br>
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