On 19/10/2011 5:25 PM, ahmet y?ld?r?m wrote:
Thanks for your reply
I dont understand "step number is at least as large as nstlist". can
you some explain?
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.
Furthermore, if the file system doesnt write the buffer to the
destination screen/file, then does that mean there is a problem? for
example
if it shows as the following:
15000000 steps, 30000.0 ps.
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.
Mark
2011/10/19 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 19/10/2011 5:04 PM, ahmet y?ld?r?m wrote:
For example;
grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr
mdrun -v -deffnm run
...
15000000 steps, 30000.0 ps.
step 100, will finish Sun Nov 27 19:11:00 2011
Sometimes it shows as the following:
15000000 steps, 30000.0 ps.
That is, there is not "will finish Sun Nov 27 19:11:00 2011"
sentence
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.
Mark
2011/10/19 Emanuel Birru <emanuel.bi...@monash.edu
<mailto:emanuel.bi...@monash.edu>>
You can get them in the log file. (At the bottom)
Cheers,
=========================================================
Emanuel Birru
PhD Candidate
Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia
Tel: Int + 61 3 9903 9187 <tel:%2B%2061%203%209903%209187>
E-mail: emanuel.bi...@monash.edu
<mailto:emanuel.bi...@monash.edu>
www.pharm.monash.edu.au <http://www.pharm.monash.edu.au>
-----Original Message-----
From: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] On Behalf Of Mark Abraham
Sent: Wednesday, 19 October 2011 3:08 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] calculation time
On 19/10/2011 5:26 AM, ahmet y?ld?r?m wrote:
> Dear users,
>
> Sometimes, in the end ( in production simulation), Gromacs
doesn't
> show calculation/finish time on screen, why? How can we
show it?
I don't know what you mean.
Mark
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Ahmet YILDIRIM
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