AMBER Archive (2005)

Subject: AMBER: implementing AMBER in NAMD

From: Lina Nilsson (linan_at_u.washington.edu)
Date: Thu Apr 28 2005 - 09:23:16 CDT

Dear all,
I am unable to get a stable MD system for use with NAMD from .crd and
.top files created with xleap. Am I making a mistake in my xleap
generation or NAMD input files?

When I create .crd and .top files in AMBER to use in NAMD MD
simulations, my periodic boxes (water and protein) blow up as soon as
the temperature is turned on (the energies, volumes etc seem to be fine
during mimimization in NAMD, as far as I can tell). First 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 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 in charmm. This may 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

The density of the system is around 0.76-0.78 g/cc, even when I use
closeness = 0.5, which is very low d / much lower than I get from
charmm. How do I deal with this? 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

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