VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 18 2010 - 16:16:06 CDT

Hi,
  From your mail, it's not clear what your real problem is.
What output do you get from VMD and NAMD when you run the "imd connect"
portion of your script below? Does NAMD wait for VMD to attach?
Do you have the NAMD host name and port specified correctly?
Are you working through one of the IMD tutorials or starting from scratch?:
  http://www.ks.uiuc.edu/Training/Tutorials/
  http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/index.html
  http://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/nanotubes-html/index.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 18, 2010 at 07:18:22PM +0000, Nuno Sousa Cerqueira wrote:
> Hello,
>
> I am having problems running imd under the shell.
>
> The alanine molecule seems to be jumping only between two conformers,
> and not as it should be expected, i.e., following the dynamic
> simulation.
>
> I use the following script:
>
>
> mol new NAMD_1/alanin.pdb type pdb
> mol addfile NAMD_1/alanin.psf type psf
> mol delrep 0 top
> mol representation Lines
> mol color ColorID 0
> mol selection {all}
> mol addrep top
> mol drawframes top 0 {now}
> mol representation Licorice 0.300000 10.000000 10.000000
> mol color Name
> mol selection {resid 7 75 539}
> mol addrep top
> mol drawframes top 1 {now}
> mol rename top GLCliq100C1bar.gro
> set viewpoints([molinfo top]) {{{1 0 0 -17.6829} {0 1 0 -18.1038} {0 0
> 1 -20.0221} {0 0 0 1}} {{0.293337 0.0118332 -0.955939 0} {-0.241153
> 0.968506 -0.0620104 0} {0.925099 0.248718 0.286952 0} {0 0 0 1}}
> {{0.0505537 0 0 0} {0 0.0505537 0 0} {0 0 0.0505537 0} {0 0 0 1}} {{1
> 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
> lappend viewplist [molinfo top]
> foreach v $viewplist {
> molinfo $v set {center_matrix rotate_matrix scale_matrix
> global_matrix} $viewpoints($v)
> }
> unset viewplist
> pbc box
> axes location off
> rock y by 0.01
> animate delete beg 0 end 0 0
> animate style rock
> animate speed 0.8
> animate forward
>
> imd connect 0 2030
>
>
> In the background i am running : namd2 alanin.conf
>
>
> Regards, Nuno 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078