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On 6/05/2011 2:06 AM, Sanku M wrote:
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<div>I found it will work if I use -b 13.9 -e 14.1</div>
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<br>
Yes, that is expected. The time for each frame has been computed by
adding up the size of each time step stored in a floating-point
variable. Such algebra is different from normal algebra - see <a
href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a>.
So some time frames will be "right" and some will be a bit out. Look
at what gmxcheck says about the frame you have obtained.<br>
<br>
Mark<br>
<br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Sanku M <a class="moz-txt-link-rfc2396E" href="mailto:msanku65@yahoo.com"><msanku65@yahoo.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>; Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b><span style="font-weight: bold;">Sent:</span></b> Thu,
May 5, 2011 10:33:19 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] trjconv problem<br>
</font><br>
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<div>Hi Justin,</div>
<div> In many of the frames, if I use -b and -e to be
same , it works</div>
<div>For example, I found if I use -b 16 -e 16, it gives
me the the snapshot at 16ps. But, in many cases like
14ps, it is not working. Also, I tried <span
class="Apple-style-span" style="font-family:
arial,helvetica,sans-serif; font-size: 13px;">-b 13 -e
14 -dump 14 . It does not work saying 'WARNING no
output, trajectory ended at 14'</span></div>
<div>Any help will be appreciated.</div>
<div>Sanku</div>
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york,times,serif; font-size: 12pt;"><br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b><span style="font-weight: bold;">Sent:</span></b>
Thu, May 5, 2011 10:22:38 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] trjconv problem<br>
</font><br>
<br>
<br>
Sanku M wrote:<br>
> Hi,<br>
> I am having a problem with trjconv to get a
single snap-shot from a trajectory file. I am using
gromacs 4.0.7 .<br>
> If I try to get a snapshot corresponding to 14
ps, I was trying to use "-b 14 -e 14 " command as
follows. But,<br>
> If I issue this command as shown below<br>
> trjconv --f traj.xtc -o conf_pep.gro -s
topol.tpr -b 14.0 -e 14.0 it crashes with following
error:<br>
> Precision of traj.xtc is 0.001 (nm)<br>
> Using output precision of 0.001 (nm)<br>
> <br>
> WARNING no output, trajectory ended at 14<br>
> <br>
> However, if I issue the same trjconv command
using "-dump 14" as shown below, trjconv provides the
correct snapshot at 14 ps:<br>
> trjconv --f traj.xtc -o conf_pep.gro -s
topol.tpr -dump 14.0 But, this "-dump 14" command
becomes extremely time consuming as I was trying to
get the snap-shot for a long time i.e around 30000ps .
So, I am trying to get "-b 14 -e 14" command work .
So, I was wondering whether you have any clue how to
get around with this.<br>
<br>
If I recall, -b and -e cannot be the same. This is
the reason for -dump. It might be worth a try to see
if trjconv -b 13 -e 14 -dump 14 speeds things up any.<br>
<br>
-Justin<br>
<br>
> Sanku<br>
> <br>
> <br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" rel="nofollow"
target="_blank" href="http://vt.edu">vt.edu</a> |
(540) 231-9080<br>
<span><span><a moz-do-not-send="true" target="_blank"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span></span><br>
<br>
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