[gmx-users] Re: Trajectory visualization

[Dommert Florian]

On Fri, 2011-04-15 at 15:15 +1000, Mark Abraham wrote:
> On 15/04/2011 3:08 PM, bharat gupta wrote: 
> > Reduicng no. of frames means breaking the simulation into smaller
> > frames ... will it affect the result ??
> 
> You can use trjconv -dt to reduce the number of frames per unit time,
> not just chopping into segments. Whether it affects your result is
> something only you can answer, because only you know what you are
> trying to do.
> 
> Mark
> 

And if you want to play a little bit around, you can also tell VMD if
you want read every step of the xtc file. In the frame section of the
molecule file browser, there is an option stride. Increase this number
and VMD will read just every n-th step and you can avoid using trjconv
for many many times.

/Flo


> > 
> > On Thu, Apr 14, 2011 at 10:06 PM, Mark Abraham
> > <Mark.Abraham at anu.edu.au> wrote: 
> >         On 15/04/2011 2:49 PM, bharat gupta wrote:
> >                 Hi,
> >                 
> >                 I have done a simulation of 10ns but while viewing
> >                 the trajectory in VMD I am getting some problems.
> >                 After loading the .gro and .xtc file VMD stops
> >                 working .. I used trjconv to compress the file but
> >                 VMD doesnot read frames from tat file... How can I
> >                 visualize the trajectories??
> >         
> >         
> >         How do you mean "does not read frames from that file"? Can
> >         you read an .xtc of one frame?
> >         
> >         Maybe VMD is running out of memory. Use trjconv to reduce
> >         the number of frames and try again.
> >         
> >         Mark
> >         -- 
> >         gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> >         Can't post? Read
> >         http://www.gromacs.org/Support/Mailing_Lists 
> > 
> > 
> > 
> > -- 
> > Bharat
> > Ph.D. Candidate
> > Room No. : 7202A, 2nd Floor
> > Biomolecular Engineering Laboratory
> > Division of Chemical Engineering and Polymer Science
> > Pusan National University
> > Busan -609735
> > South Korea
> > Lab phone no. - +82-51-510-3680, +82-51-583-8343 
> > Mobile no. - 010-5818-3680
> > E-mail : monu46010 at yahoo.com 
> > 
> 
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110415/b5adbf67/attachment.sig>