From: Sonu Kumar (sonu2kd_at_gmail.com)
Date: Thu Jul 21 2016 - 00:52:55 CDT
I have been trying to do a md simulation for my polymer with the help of
NAMD in a periodic box of 24.955 Angstroms.
I took the minimized molecule and wrapped it with the help of VMD along the
center of mass in a box of 24.955 A. I extracted the pdb for this and used
this file in simulation so that no bond crosses the boundary of the
Then I ran the md simulation for this pdb file with configuration listed at
the end. However, the output which I received showed bonds sticking out
despite the fact WRAPALL WAS ON(just emphasizing). I tried everything like
increasing or decreasing minimization or doing it in many steps wrapping it
along every step.
However, everytime bonds sticked out of the box.
Can you help me in solving this problem of why wrapAll is not working.
Moreover, is it alright to choose lesser values of cutoff, switchdist and
pairlistdist as it was showing patch grid error for 25 A box.
Configuration file :
set temperature 298
cellBasisVector1 17.69565 0 0
cellBasisVector2 0 18.89368 0
cellBasisVector3 0 0 24.77155
cellOrigin 5.054398 6.476589 12.377248
#Chose lesser values because of patch grid error for 25 A box
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds none ;# needed for 2fs steps
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen no ;# don't couple langevin bath to hydrogens
restartfreq 500 ;# 500steps = every 1ps
run 100000 ;# 200ps
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