Problems with wrapAll

From: Sonu Kumar (
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.
For this,
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
periodic box.

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 :

structure final.psf
coordinates haha1.pdb
outputName sonu12345

set temperature 298

firsttimestep 0

paraTypeCharmm on
parameters par_all22_prot.prm

temperature $temperature

cellBasisVector1 17.69565 0 0
cellBasisVector2 0 18.89368 0
cellBasisVector3 0 0 24.77155
cellOrigin 5.054398 6.476589 12.377248

#wrapWater on
wrapAll on

exclude scaled1-4
1-4scaling 1.0
cutoff 4.9
switching on
switchdist 4.0
pairlistdist 5.0
#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
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

minimize 1000
reinitvels $temperature

run 100000 ;# 200ps

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