[gmx-users] trjconv problem

[Mark Abraham]

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 <msanku65 at yahoo.com>
> *To:* jalemkul at vt.edu; Discussion list for GROMACS users 
> <gmx-users at 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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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
>
> ========================================
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