On 6/05/2011 2:06 AM, Sanku M wrote:
I found it will work if I use -b 13.9 -e 14.1
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
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic. 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.
Mark
------------------------------------------------------------------------
*From:* Sanku M <msank...@yahoo.com>
*To:* jalem...@vt.edu; Discussion list for GROMACS users
<gmx-users@gromacs.org>
*Sent:* Thu, May 5, 2011 10:33:19 AM
*Subject:* Re: [gmx-users] trjconv problem
Hi Justin,
In many of the frames, if I use -b and -e to be same , it works
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 -b 13 -e 14 -dump 14 . It does not work saying 'WARNING
no output, trajectory ended at 14'
Any help will be appreciated.
Sanku
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Thu, May 5, 2011 10:22:38 AM
*Subject:* Re: [gmx-users] trjconv problem
Sanku M wrote:
> Hi,
> I am having a problem with trjconv to get a single snap-shot from a
trajectory file. I am using gromacs 4.0.7 .
> If I try to get a snapshot corresponding to 14 ps, I was trying to
use "-b 14 -e 14 " command as follows. But,
> If I issue this command as shown below
> trjconv --f traj.xtc -o conf_pep.gro -s topol.tpr -b 14.0 -e
14.0 it crashes with following error:
> Precision of traj.xtc is 0.001 (nm)
> Using output precision of 0.001 (nm)
>
> WARNING no output, trajectory ended at 14
>
> However, if I issue the same trjconv command using "-dump 14" as
shown below, trjconv provides the correct snapshot at 14 ps:
> 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.
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.
-Justin
> Sanku
>
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
