Qestions about NPT simulations.

From: Lv Shouqin (shouqinlv_at_hotmail.com)
Date: Wed Jan 26 2005 - 07:29:47 CST

Dear All,
I have two questions about simulations of NAMD:
1) I know I am not the first to ask this kind of question, but I did not
get any clear answer from NAMD-L, my question is: what¡¯s the relationship
among ¡°cellvectors¡± ¡°cellsizes¡± and ¡°PMEgridSizes¡±? my system is x:
-12 ~ 140, y: -12 ~ 52, z: 198 ~ 267, in my opinion, the cellvectors are:
140.0 0 0; 0 52.0 0; 0 0 267 respectively with the cellorigin (64.0 20.0
232.5), cellsizes are: 152.0 x 64.0 x 69.0.
Then how can I decide the PMEgridSizes? Or what¡¯s the rules for setting up
the PMEgridSizes? (except the factors of 2, 3, 5)
2) Based on the system mentioned above, I want to run minimization,
increasing temperature and NPT relaxation simulations. Unfortunately, the
shape deformed greatly. What¡¯s wrong with this? Is my scripts not correct?
Or need more constraints to keep the shape? The followed scripts are my
configuration file for NPT simulation:
#the relaxation process
# molecular system
structure t-s-ana-2-third.psf
coordinates t-s-ana-2-third.pdb
bincoordinates t-s-ana-2-equil11restart.coor
binvelocities t-s-ana-2-equil11restart.vel
extendedSystem t-s-ana-2-equil11restart.xsc
# forcefield
paraTypeCharmm on
parameters t-s-analogy-forcefield/par_all27_prot_lipid.prm
parameters t-s-analogy-forcefield/par_all22_sugar-ana-1.inp
dielectric 1.0
exclude scaled1-4
1-4scaling 1.0
# approximations
seed 1081407385
timestep 1.0
fullElectFrequency 4
switching on
switchDist 11
cutoff 14
pairlistdist 15
stepsPerCycle 20
# output frequency control
outputEnergies 1000
outputTiming 1000
outputPressure 1000
DCDfreq 4000
velDCDfreq 50000
XSTfreq 4000
binaryoutput off
outputname t-s-ana-2-equil12-1_out
restartname t-s-ana-2-equil12-1restart
XSTfile t-s-ana-2-equil12-1_out.xst
restartfreq 100000
# period boundary condition
cellBasisVector1 140.0 0 0
cellBasisVector2 0 52.0 0
cellBasisVector3 0 0 267.0
cellOrigin 64.0 20.0 232.5
wrapWater on

# PME alogrithm
PME on
PMEGridSizeX 150
PMEGridSizeY 64
PMEGridSizeZ 72

# keep the heat bath
langevin on
langevinTemp 300
langevinDamping 0.5

# keep the barostat
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 300

useGroupPressure yes

# fixed control
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile t-s-ana-2-eq-158ca-fix.pdb
fixedAtomsCol B

firsttimestep 0
run 100000
Thanks a lot! Any comment is welcomed!
Regards,
Shouqin Lv

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