[gmx-users] Re: Trajectory visualization
dommert at icp.uni-stuttgart.de
Fri Apr 15 09:37:19 CEST 2011
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.
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.
> > 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
> > --
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> > --
> > Bharat
> > Ph.D. Candidate
> > Room No. : 7202A, 2nd Floor
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Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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