From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Mon Jan 08 2007 - 12:35:07 CST
Hi All,
I am trying to simulate a protein with a calcium ion and ligand attached
using Amber forcefield in namd for 1ns, in two instances.
Case1: Simulating the protein with Calcium attached in 10A water box
Case2: Simulate the protein complex with inhibitor in a 10A water box
In both the cases, right from frame 0, (I minimize for 1000 steps) the
protein comes out of the water box and tethers to one edge, while the
calcium ion and ligand comes out and tethers themselves to two other edges
of the box. In other words they are partially immersed (just anchorched) to
the water box on 3 different sides. Initially i thought it might be the
parameters of Ca or ligand that is causing this, so I tried simulating the
protein alone w/o Ca2+ even, it does the same thing, the protein comes out
and even translates to another edge of the box after some 1000 frames
randomly.
The following is my .config file. Any guidance will be much appreciated.
amber yes
parmfile fxa_wat_ca.prmtop
ambercoor fxa_wat_ca.inpcrd
set temperature 310
set outputname outFxa_ca
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm off
temperature 0
reassignFreq 1000
reassignTemp 25
reassignIncr 25
reassignHold 310
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ; # 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
margin 5
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 310
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 69.0 0. 0.
cellBasisVector2 0. 76. 0.
cellBasisVector3 0. 0. 66.1230010986
cellOrigin -0.0838125869632 0.121281333268 -0.300958424807
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 70
PMEGridSizeY 80
PMEGridSizeZ 70
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 310
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 150
outputPressure 150
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels 310
run 500000 ;# 1000ps
-- -Rima
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:18 CST