restart a NAMD simulation after coordinate transformation in VMD

From: Vlad Cojocaru (
Date: Fri Oct 26 2007 - 04:47:11 CDT

Dear NAMD users,

I am trying to perform a simulation in which tclforces are used to move
a small part of the system with a ct velocity along a direction. The
center of mass of the other part of the system is constrained to the
initial position by applying an SMD with v=0.

As I read, such a procedure may be applied only if the SMD with v=0 is
applied along x, y or z axis. I chose the x axis for that. Thus, the
force from tclforces will also be applied on the x axis. For that I
needed to apply some coordinate transformations to align the tcl force
direction along the x axis. I did that using the VMD script below.

Before running my simulation, for a test, I tried to run a standard NPT
simulation using the transformed coordinates (a.pdb at the end of the
VMD script). To my surprise, the simulation fails to even start and the
error "atoms moving too fast" appears right before ts=0 output. Now, the
same simulation runs properly if instead of the transformed coordinates
I used the original coordinates (a_rst.coor). However, the transoformed
coordinates look absolutely fine when loaded in VMD or other software
with the corresponding topology file (

Obviously NAMD has some problems in using the transformed coordinates
for the simulation. I would like to ask you if anybody has observed such
a behaviour before and could give me an advice on how to fix this. Also,
if you think of easier ways to do these tasks please let me know (maybe
one could do the coordinate transformations directly in NAMD ...)

Thank you in advance for any suggestions

Best wishes

---VMD script to transform coordinates ----

mol load parm7
mol addfile a_rst.coor type pdb
set all [atomselect top "all"]
set sel1 [atomselect top "resid 230"]
set center_sel1 [measure center $sel1]
set sel2 [atomselect top "name CA and resid 76 192"]
set center_sel2 [measure center $sel2]
set smd_dir [vecnorm [vecsub $center_sel2 $center_sel1]]
puts "Direction of force is $smd_dir"
set tm1 [transvecinv "$smd_dir"]
$all move $tm
unset all
set all [atomselect top "all"]
set center [measure center $all]
set tm2 [trans origin "$center"]
$all move $rm2
$all writepdb a.pdb

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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