From: aravind chandrasekaran (gandhiaravind_at_gmail.com)
Date: Mon Jul 29 2013 - 06:24:31 CDT
Hey hi,
I tried to calculate INITIAL forces on individual atoms \Sigma_{i} F_{i,j}
using
loadtotalforces function of NAMD. NAMD tutorial suggests that the function
outputs forces of the previous instant/time step. I asked it to output the
forces at step1. I used the following configuration file.
# Integrator Parameters
timestep 0.00000000000001
.........
......
## EXECUTION SCRIPT ##
tclForces on
tclForcesScript {
for {set i 1} {$i<=4796} {incr i} {
addatom $i
}
proc calcforces {} {
set step [getstep]
if { $step== 1 } {
loadmasses m
loadtotalforces f
set thefile [open 1D9Vmi10_step_L_unbound.txt w]
set fmt1 "%20.12f%20.12f%20.12f%20.12f"
for {set i 1} {
$i<=4796} {incr i} {
puts $thefile [format $fmt1 $m($i) [lindex $f($i) 0] [lindex $f($i) 1]
[lindex $f($i) 2]]
}
}
}
}
run 1
When I change the time step to 10 fs from 1 fs, I see that the output
forces are different. If at step1, it writes the forces calculated based on
initial conditions, the results should be the same even if the time step
changes.
In addition, I also tried changing the IF condition to step==0 to see the
output. I get an error message that NAMD couldn't read f(1) force (on atom
1) information.
Hence, I would like to know how to obtain initial forces from NAMD.
-Aravind.
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