VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 18 2010 - 16:54:42 CDT

On Thu, 2010-03-18 at 19:18 +0000, Nuno Sousa Cerqueira wrote:
> Hello,
>
> I am having problems running imd under the shell.

what 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

not that it makes a difference, but these two lines
should be the other way around.

> 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

why animate here?

>
> imd connect 0 2030

i the machine running NAMD called "0"?
i seriously doubt that. RTFM!
this should be something like:
imd connect my.machine.somewhere.net 2030

> In the background i am running : namd2 alanin.conf

if it is local, then of course the machine
name could be "localhost" or "127.0.0.1"

cheers,
  axel.

>
> Regards, Nuno
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.