problems of "Stray PME grid charges"

From: pxq ѩ (pxq_at_dicp.ac.cn)
Date: Tue Sep 08 2009 - 09:40:44 CDT

Hello everyone,

When running simulation of a trans-membrane protein with NAMD2.6,I got the following warning and error.
 
"ERROR: Stray PME grid charges detected: 3 sending to 7 for planes 89
Warning: Stray PME grid charges ignored!"

I have tried to:
1. Lower the final temperature ( from 310K to 300K)
2. Increase the PME grid parameters (from 80 90 120 to 90 90 128)
3. Lower the constraints (from 500 to 50 and then 30)
4. Chang the Periodic Boundary conditions (from 69 82 114 to 67 80 112)
5. Increase the PME cutoff form 10 to 12 and then 14

What is more, this system can run smoothly with amber.

However, these errors and warnings are still there.

So, I eagerly need your help with this problem.

Any suggestion is greatly welcomed.

Thanks very much

My input cript is as follows

#amber force field parameters
amber yes
parmfile $mol.prmtop
ambercoor $mol.inpcrd
outputname $mol$N
readexclusions no

# frequencies
outputEnergies 100
restartfreq 100

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333
cutoff 14.
switching on
switchdist 12.
pairlistdist 15.5

# Periodic Boundary conditions
if {1} {
cellBasisVector1 67. 0. 0.
cellBasisVector2 0. 80. 0.
cellBasisVector3 0. 0 112.
cellOrigin -2.9445 5.1257 7.1837
}
wrapWater on
wrapAll on

#PME
if {1} {
PME yes
PMEGridSizeX 90
PMEGridSizeY 90
PMEGridSizeZ 128
#PMEGridSpacing 1
}

###################################################
#################for MD simulations################
###################################################

if {1} {
#numsteps 20000

#
timestep 2.0
rigidBonds all ;
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidDieOnError on

#
firsttimestep 0

#
temperature $temperature

#
dcdfile $mol$N.dcd
dcdfreq 100
}
# Constant Temperature Control
if {1} {
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
}

# Constant Pressure Control
if {0} {
useGroupPressure yes ;
useFlexibleCell yes ;
useConstantArea no ;

langevinPiston on
langevinPistonTarget 1.01325 ;
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
SurfaceTensionTarget 60.0 ;

#harmonic constraints
if {1} {
constraints on
consref $mol-fixed.pdb
conskfile $mol-fixed.pdb
conskcol O
}

# Minimization
if {1} {
minimize 5000
reinitvels $temperature
}

run 50000 ;# 100ps

(END)

===================================================================================================
 Pang Xueqin
 State Key Laboratory of Molecular Reaction Dynamics
 Dalian Institute of Chemical Physics
 Chinese Academy of Sciences.
 Tel: +86-411-84379352 Fax: +86-411-84675584
 http://www.english.dicp.ac.cn/
===================================================================================================

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