From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Sat Apr 20 2002 - 21:28:49 CDT
Thanks snoze pa! I'll try it.
--Sting
=================================
try to run each part seperately.
1. minimization.
2. equlib.
3. free md
goodluck
On 4/19/02, Sting <stg1979_at_emails.bjut.edu.cn> wrote:
Dear All,
I am using namd to study trihelices in the water box. Minimization and 500ps CA restrained dynamics were performed. I found a strange phenomenon: sevral holes without water formed in the water box(even afer adding the water layer to 15 angstrom),and with the rotating of the trihelices,the holes seem moving accordingly. Still when performing SMD,the water holes remain and adjust while going on. I wondered how to explain it and how to tackle the problem. Could anyone offer some help? Thanks.
==========
#forcefield
paratypecharmm on
parameters par_all27_prot_lipid.inp
#molecules
structure solvated.psf
coordinates solvated.pdb
temperature 310
#temp & pressure coupling
langevin on
langevinTemp 310
langevinDamping 1
useGroupPressure yes
#output
outputname mini_eq
outputEnergies 10
restartfreq 500
DCDfreq 500
binaryoutput no
binaryrestart yes
outputTiming 100
wrapAll on
wrapNearest off
wrapWater on
#integrator
timestep 2
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 12
switching on
switchdist 10
pairlistdist 14
#margin 3
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
dielectric 1.0
PME on
cellBasisVector1 90.045 0 0
cellBasisVector2 0 32.650 0
cellBasisVector3 0 0 32.853
cellOrigin 441.652 0.379 0.0423
PMEGridSizeX 90
PMEGridSizeY 32
PMEGridSizeZ 32
#
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_ca.pdb
fixedAtomsCol B
#
minimize 0
#
minimize 10000
#
run 250000
Sting
stg1979_at_emails.bjut.edu.cn
2006-04-20
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:57 CST