Re: Problems with wrapAll

From: Sonu Kumar (sonu2kd_at_gmail.com)
Date: Fri Jul 22 2016 - 06:58:13 CDT

That was a mistake. Btw I don't quite get how to do what you suggest.
Actually the molecule is larger than the pbc and its polymer.
I have written both the conf files. Can you suggest what I must add. I have
further elaborated it down.

I have a polymer molecule of 1806 atoms with a density of 0.9.
The molecule has been minimized for 5 ns and has dimensions 38*32*26.

As per density I want to force it in a box of 25*25*25. However, upon
wrapping it using pbctools and generating the pdb which is further used in
the md simulation it is showing error probably because of bad contacts.

Can you please suggest me how to perform md simulation on this molecule by
forcing it in a box smaller than this. It shall be helpful if you can just
tell the part of script that I must add in my configuration file. I have
pasted the two configuration files I am using. Please tell what I should
add in either of these two to achieve what I want.

FIRST CONF FILE :

#My configuration file for minimization of the initial pdb :(please tell
what I should add):

structure Poly.psf
coordinates Poly.pdb
outputName first

set temperature 298
firsttimestep 0

paraTypeCharmm on
parameters par_all22_prot.prm

temperature $temperature
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# 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

if {1} {
minimize 1000
reinitvels $temperature
}

run 2500000

SECOND CONF FILE :(FOR PBC)

structure final.psf
coordinates minimized.pdb
outputName sample

set temperature 298

firsttimestep 0

margin 0

paraTypeCharmm on
parameters par_all22_prot.prm

temperature 0
reassignFreq 1000
reassignIncr 10
reassignHold 300

if {1} {
cellBasisVector1 24.954999923706055 0 0
cellBasisVector2 0 24.954999923706055 0
cellBasisVector3 0 0 24.954999923706055
cellOrigin 12.9974365234375 13.76833438873291 11.9735107421875
}
wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 15.0
switching on
switchdist 13.0
pairlistdist 17.5

# Integrator Parameters
timestep 1.0 ;# 2fs/step
rigidBonds none ;# needed for 2fs steps
#rigidTolerance 0.0005
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0

#manual grid definition
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
}

langevin off ;# 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

if {1} {
minimize 1000
reinitvels $temperature
}

run 100000

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