VMD-L Mailing List
From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri Mar 27 2015 - 13:26:01 CDT
True. This approach, however, has a downside that you still have to load your trajectories once. When simulation system is large, this process can be really slow. catdcd approach is fast and moreover, you can specify all of your input files at once at get a single trajectory file for your selection. The only "problem" with catdcd approach is that it requires a little bit of coding in VMD (tcl) & shell.
> On Mar 27, 2015, at 12:38 PM, Ajasja LjubetiÄ <ajasja.ljubetic_at_gmail.com> wrote:
> You can also do everything from VMD.
> Load just the first N frames. Save a pdb of protein only. Save a DCD of protein only.
> delete all frames and load the next N and only the protein to the next DCD file.
> If you only have to load two or three pieces this might be more convenient.
> Best regards,
> On 27 March 2015 at 17:55, Maxim Belkin <mbelkin_at_ks.uiuc.edu <mailto:mbelkin_at_ks.uiuc.edu>> wrote:
> Hi Jevgenij,
> You have to use catdcd for that purpose. The procedure is the following:
> 1. Load psf + pdb
> 2. Make a selection: set sel [atomselect top "selection text"]
> 3. Write psf of that: $sel writepsf selection.psf
> 4. Write indices of the selection:
> set ch [open indices.txt w]
> puts $ch [$sel list]; # [$sel list] is same as [$sel get index]
> close $ch
> 5. Use catdcd to extract your selection from the trajectory:
> catdcd -o output_file.dcd -otype dcd -i indices.txt trajectory_file
> Good luck,
> > On Mar 27, 2015, at 11:43 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu <mailto:jraskato_at_ucsc.edu>> wrote:
> > Dear users, I am loading a large simulation of a protein in a waterbox into vmd, and would like to only load the protein portion, because otherwise my computer crashes. I understand that one can display the protein only portion, but how about editing it prior to loading, so as to maximize performance?
> > Thanks
> > --
> > Dr. Jevgenij A. Raskatov
> > Assistant Professor in Chemistry and Biochemistry
> > Tel.: +1-831-459-2978 <tel:%2B1-831-459-2978>
> > Department of Chemistry and Biochemistry
> > Physical Science Building 356
> > 1156 High Street
> > Santa Cruz, CA
> > 95064 USA