VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Apr 29 2003 - 19:41:47 CDT

Hi,

I hope someone can help me with these two issues as I totally do not
understand the origin of the error.
1. I am trying to run the configuration file below on my local machine
(octane dual) using mpi and I get the following error message:

FATAL ERROR: berendsenPressureFreq must be a multiple of both
fullElectFrequency and nonbondedFrequency

MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
[1] Exit 1 mpirun -np 1
/stor/ioana/software/NAMD_2.5b1_Origin2000-MPI/namd2 ... |&tee
comb_namd.out
       Done

The berendsenPressureFreq is set to 4, the fullElectFrequency is 4 and the
nonbondedFrequency is 2. So it is a multiple of both fullElect and
nonbonded frequencies.
The manual says that the default value (if used, which is my case) for
berendsenPressureFreq is fullElectFrequency or nonbondedFrequency. However
if I do not define berendsenPressureFreq in the input file the program
will not run

2. Secondly I am trying to combine more namd runs in the same
configuration file (see below). For example first a cuple of steps of
minimization followed by some NPT dynamics.
The program will run the minimization but will not proceed to the next
step and also run the dynamics. I see from the example on Building
Gramicidin A that this should be possible, however it does not seem to
work.

Any advice would be greatly appreciated. Thanks,
Ioana

#Configuration file for NAMD, NPT run trying to equilibrate a water box
#at 300K

# initial config
amber on
parmfile /stor/ioana/ahl_namd/water_test_NAMD/spcWatBox.prmtop
coordinates /stor/ioana/ahl_namd/water_test_NAMD/Shake_min_WatSpc/shake_minWat.restrt.coor
temperature 0
seed 314159

exclude scaled1-4
1-4scaling 0.8333 #=1/1.2 from Amber
scnb 2.0 #this is for the van der waals

outputTiming 100
outputname test_min
outputEnergies 10
DCDfreq 100
XSTfreq 100
wrapAll on
wrapNearest on

switching on
switchdist 7.0
cutoff 9.0
pairlistdist 10.5

fullElectFrequency 4
nonbondedFreq 2
BerendsenPressureFrequency 4

#constant pressure simulation
BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 44.6e-6
BerendsenPressureRelaxationTime 10

#pressure control with SHAKE
useGroupPressure yes
useFlexibleCell yes
useConstantRatio yes

# use heuristic update that povides update about every 10 steps
stepspercycle 20

# periodic cell
cellBasisVector1 22.1824 00.00 00.00
cellBasisVector2 00.00 21.8357 00.00
cellBasisVector3 00.00 00.00 22.297
cellOrigin 11.0912 10.9178 11.148

# full electrostatics
Pme on
PmeGridSizeX 32
PmeGridSizeY 32
PmeGridSizeZ 32

# integrator params
timestep 1.0

#Amber uses rigid water and SHAKE H-bonds.
rigidBonds all

# get into batch mode
minimize 0

#minimize the system
minimize 40

#run some dynamics
outputname water_comb
numsteps 3000