From: Lina Nilsson (linan_at_u.washington.edu)
Date: Wed Apr 13 2005 - 03:16:45 CDT
Dear all,
I need to use AMBER force fields in NAMD, but from .crd and .top files
created with xleap, I can't get a system that is stable in my NAMD
simulation (tried with a protein I have previously simulated fine using
Charmm, and with a two amino acid 'test protein.') Do I need to do extra
minimzation steps when using AMBER? Other ideas????
Details:
My periodic boxes (water and protein) blow up as soon as I begin to
increase the temperature above 0 K in NAMD (the energies, volumes etc
seem to be fine/plateau during mimimization in NAMD, as far as I can
tell). With the temp turned on, the system volume shrinks rapidly, only
to then start increasing and then 'blowing up' as atoms start moving too
fast for the simulation to handle (the temperaure is increasing rapidly
too, of course).
The NAMD base scripts I use work fine for charmm ff based simulations.
The densities I get from the xleap prep are low (<0.8 g/cc)compared to
what I get solvating my charmm systems. Reducing the closeness factor in
xleap to 0.5 doesn't help. May the low density be causing instabilities?
Turning on RigidBonds reduces the problem, but does not get rid of it,
for what that is worth. I am completely stuck on this and ANY input is
much appreciated!
Lina
TWO AMINO ACID TEST CASE
XLEAP:
xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff # tried ff03 and then ff94
filename = loadpdb PDB.pdb
solvatebox filename TIP3PBOX 16
charge filename # --> no charge
check filename
# --> no errors. "Unit is ok" Some hydrogens are too close to each other
saveamberparm filename filename.top filename.crd
savepdb filename filename.pdb
# Other than the water density, the system looks fine in VMD (no missing
atoms etc).
THEN MINIMIZING IN NAMD in 3 steps (first water only, then holding
protein backbone still, then all atom minimization):
cwd ./
amber on
readexclusions no
parmfile ff94_xxx.top
coordinates ff94_xxx.pdb
restartname xxx.rst
restartfreq 100
binaryrestart yes
outputname xxx
binaryoutput no
DCDfile xxx.dcd
DCDfreq 100
outputEnergies 1
outputMomenta 1
outputPressure 1
XSTfile xxx.xst
XSTfreq 100
numsteps 2000
timestep 1.0
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fixedAtoms.pdb
fixedAtomsCol B
stepspercycle 4
nonbondedFreq 1
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.0
exclude scaled1-4
1-4scaling 0.833333
fullElectFrequency 4
PME yes
PMETolerance 0.000001
PMEInterpOrder 4
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 36
scnb 2
temperature 0
dielectric 1.0
cellBasisVector1 34.572 0 0
cellBasisVector2 0 33.2880 0
cellBasisVector3 0 0 33.2840
cellOrigin -0.1518 0.1325 -0.0739
wrapWater on
constraints off
minimization on
--> output *eems* ok...
FINALLY, THERMALIZING:
cwd ./
amber on
readexclusions no
parmfile ff94_xxx.top
coordinates minoutput.coor
extendedSystem minoutput.xsc
restartname xxx.rst
restartfreq 100
binaryrestart yes
outputname xxx
binaryoutput no
DCDfile xxx.dcd
DCDfreq 100
outputEnergies 100
outputMomenta 100
outputPressure 100
XSTfile xxx.xst
XSTfreq 100
numsteps 40000
timestep 1.0
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fixedAtoms.pdb
fixedAtomsCol B
stepspercycle 4
nonbondedFreq 1
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.0
exclude scaled1-4
1-4scaling 0.833333
fullElectFrequency 4
PME yes
PMETolerance 0.000001
PMEInterpOrder 4
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 36
scnb 2
temperature 0
dielectric 1.0
reassignFreq 1000
reassignTemp 10.0
reassignIncr 10.0
reassignHold 310.0
useGroupPressure no
useFlexibleCell no
BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 0.000045
BerendsenPressureRelaxationTime 1000
BerendsenPressureFreq 4
wrapWater on
constraints off
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:40 CST