Re: conf file script ( help needed )

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sat Jun 04 2011 - 07:53:08 CDT

 
A Friend of mine Ranyere Deyler help me with similar problem. Thanks for him for this script.
 
Maybe it could help you.
 
The steps are just a gess. You must change it if you want a slow/fast anneal.
 
Regards,
 
Flavio
 
 
#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################

structure            PROT_wb.psf
coordinates        PROT_wb.pdb

set temperature    300
set outputname     PROT_wb_eq

firsttimestep      0

#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm        on
parameters          par_all27_prot_lipid_na.inp
temperature         $temperature

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        13.5

# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2 
stepspercycle       10

# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1    86.     0.    0.
cellBasisVector2     0.   100.5   0--0-1709863495-1307191988=:29463--

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