TMD and binary coordinate files

From: Bryan Roessler (roessler_at_uab.edu)
Date: Wed Sep 28 2011 - 16:40:49 CDT

Hello,

I am trying to set up a TMD simulation using a previously-heated molecule
and the binary coordinates from that simulation thereof. I have set the
occupancy column of both the starting and targeted PDB files to 1, but I do
not think this value is being passed to NAMD when I have the bincoordinates
option active. In my output file, I get the following line, which leads me
to believe that the TMD atoms are not being selected:

Info: Startup phase 7 took 1.20972 s, 592.59 MB of memory in use
> Info: CREATING 27048 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> *Info: 0 TMD ATOMS*
> Info: Startup phase 8 took 1.82281 s, 613.238 MB of memory in use
> Info: Startup phase 9 took 0.000179052 s, 613.238 MB of memory in use
> Info: Finished startup at 16.9887 s, 613.238 MB of memory in use

I have tried saving the binary coordinates to a pdb file, and then using
that pdb file as my input without the binary coordinates option, but I get
RATTLE constraint failures if I do it this way. I have a starting
temperature of 310K.

Ideas?

Thanks,

Bryan Roessler
The University of Alabama at Birmingham

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:25 CST