VMD-L Mailing List

From: Nuno Sousa Cerqueira (nscerque_at_fc.up.pt)
Date: Thu Mar 18 2010 - 14:18:22 CDT

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