From: msa5 (msa5_at_rice.edu)
Date: Thu Nov 17 2016 - 11:06:48 CST
Dear NAMD users;
I am simulating water/n-alkane to study the Interfacial Tension. My
system contains three layers (water/n-alkane/water). Each water layer
has 2506 molecules and the n-alkane has 200 molecules.
The simulation box is 50x ,50y and 90z direction ( 50x, 50y, 30z for
each layer ).
a) I initially ran the simulation for equilibration by using NPT over
500000 steps ( the volume was completed converged ).
b) I continued the simulation by using NVT to generate the data over
2,000,000 steps.
The dcd file was generated successfully, the density profile looks
good. After that I used the blow script to compute the pressure
tensors , but I am getting this error ( Reason: FATAL ERROR: Low
global exclusion count! (71264 vs 71268) System unstable or
pairlistdist or cutoff too small.)
I've been increasing the cutoff and pairwise gradually and accordingly
but the problem still exists.
I would really appreciate any feedback.
Thanks a lot in advance
Mohamed
The script is below :
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Simulation NVT
# a Water/Dodecane/Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure dode_tip4p.psf
coordinates dode_tip4p.pdb
#set temperature 383
outputname pressure
# continuing a run
set inputname dode_tip4p_NVT
binVelocities $inputname.vel
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all36_ethers.prm
parameters tip4p.par
waterModel tip4
# Periodic Boundary Conditions
cellBasisVector1 50.0 0.0 0.0
cellBasisVector2 0.0 50.0 0.0
cellBasisVector3 0.0 0.0 90.0
#cellOrigin 0 0 0
cellOrigin 25.0 25.0 45.0
#wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 52
PMEGridSizeY 52
PMEGridSizeZ 92
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 14
cutoff 16
pairlistdist 18
pressureProfile on
pressureProfileSlabs 30
pressureProfileFreq 100
pressureProfileAtomTypes 6
pressureProfileAtomTypesFile dode_tip4p.pdb
pressureProfileEwald on
pressureProfileEwaldX 16
pressureProfileEwaldY 16
pressureProfileEwaldZ 16
set ts 0
firstTimestep $ts
coorfile open dcd Dode_tip4p_NVT.dcd
while { [coorfile read] != -1 } {
incr ts 500
firstTimestep $ts
run 500000
}
coorfile close
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:49 CST