RE: cell basis vector restart

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue Mar 02 2010 - 12:09:07 CST

Now I am getting this error, and I am not totally sure what it means:

Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

This is the .namd file from the first job where I heat the system and the box grows:

amber yes
parmfile kfretBlysA.prmtop

# Le coordinate sono lette dal file pdb.
# In questo modo si eleina la
# dipendenza da ambercoord etc....

coordinates kfretBlysAmin.coor
scnb 2.0

# output
set output kfretBlysAheat
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 2000
xstFreq 2000

binaryoutput no
binaryrestart no
outputEnergies 200
restartfreq 10000 #makes restart files (xsc, coor, vel) every x steps

# Basic dynamics
exclude scaled1-4 #neglect 1-2, 1-3 estatic? interactions, weaken 1-4
1-4scaling 0.8333 #between 0-1 0: neglect 1-4 estatic interactions
COMmotion no #??
dielectric 1.0 # 1.0 is default?

# Simulation space partitioning
switching on
switchdist 10 #starts smoothly lowering vdw curve at this distance
cutoff 12 #vdw ignored after this distance
pairlistdist 14 #only looks for possible close atoms in this distance

# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20 #frequency with which atoms within cutoff are looked for
nonbondedFreq 1 #full nonbonded interactions calculated only every x steps
fullElectFrequency 1 #full estatics calculated only every x steps
rigidBonds water # no vibration, change in bond length

# Temperature control

# set temperature 298
temperature 0 # initial temperature
reassignfreq 1000
reassigntemp 0
reassignincr 10
reassignhold 300

cellBasisVector1 -62.0900006295 0.0 0.0
cellBasisVector2 0.0 -59.0930003524 0.0
cellBasisVector3 0.0 0.0 -68.6139990091
cellOrigin 32.4652252197 30.272726059 35.9197502136
wrapAll on
dcdUnitCell yes
useConstantArea no # CAMBIATO

PME yes
PMEGridSizeX 65
PMEGridSizeY 60
PMEGridSizeZ 70

# additional simulation parameters--fixed atoms
fixedAtoms on
fixedAtomsForces on
fixedAtomsCol B
fixedAtomsFile kfretBlysAfix.pdb

#constraints on
#consref kfretBlysAharmref.pdb
#conskfile kfretBlysAharm.pdb
#conskcol B

# Scripting

minimize 1000
#reinitvels $temperature
#run 10000
#reinitvels $temperature
#run 10000
#reinitvels $temperature
#run 10000
#reinitvels $temperature
#run 10000
#reinitvels $temperature
#run 10000

## I primi 50 ps sono stati eseguiti nell'insieme NPT
## riassegnando le velocit ogni 10 ps

## Seguono 5 ns di simulazione NPT
# su cui farai le analisi
run 40000

Do I need to put in a keyword to keep the volume constant, or something?

This is the .namd file from the next job where I got the error:

# input
amber yes
parmfile ../kfretBlysA.prmtop

# Le coordinate sono lette dal file pdb.
# In questo modo si eleina la
# dipendenza da ambercoord etc....

#coordinates klechHmin.coor

set inputname kfretBlysAheat
Coordinates $inputname.coor
Velocities $inputname.vel
extendedSystem $inputname.xsc

scnb 2.0

# output
set output kfretBlysArun
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 2000
xstFreq 2000

binaryoutput no
binaryrestart no
outputEnergies 200
restartfreq 10000 #makes restart files (xsc, coor, vel) every x steps

# Basic dynamics
exclude scaled1-4 #neglect 1-2, 1-3 estatic? interactions, weaken 1-4
1-4scaling 0.8333 #between 0-1 0: neglect 1-4 estatic interactions
COMmotion no # ??
dielectric 1.0 # 1.0 is default?

# Simulation space partitioning
switching on
switchdist 10 #starts smoothly phasing out vdw curve at this distance
cutoff 12 #vdw ignored after this distance
pairlistdist 14 #only looks for possible close atoms in this distance

# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20 #frequency with which atoms within cutoff are looked for
nonbondedFreq 1 ##full nonbonded interactions calculated only every x steps
fullElectFrequency 2 #full estatics calculated only every x steps
rigidBonds water # no vibration, change in bond length

# Temperature control

set temperature 298

# Langevin Dynamics
langevin on; # do langevin dynamics
langevinDamping 5; # damping coefficient (gamma) of 5/ps
langevinTemp $temperature; # bath temperature
langevinHydrogen no; # don't couple langevin bath to hydrogens
seed 12345

# Pressure control
langevinPiston on
langevinPistonTarget 1.01325; # in bar -> 1.01325 bar = 1 atm
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp $temperature
useFlexibleCell no # CAMBIATO (cell dimensions vary independently. useful for membranes)
useGroupPressure yes # must be set to yes if rigidbonds is set

# PBC

if (0) {
cellBasisVector1 -63.3060009479 0.0 0.0
cellBasisVector2 0.0 -59.0939998031 0.0
cellBasisVector3 0.0 0.0 -72.3179966211
cellOrigin 32.7434005737 30.3597278595 37.5696868896
}
wrapAll on
dcdUnitCell yes
useConstantArea no # CAMBIATO

PME yes #shoud PME part be commented out on restart? email says no.
PMEGridSpacing 1.0 #automatically selects appropriate PME dimensions
#PMEGridSizeX 65
#PMEGridSizeY 60
#PMEGridSizeZ 75

# additional simulation parameters--fixed atoms
fixedAtoms on
fixedAtomsForces on
fixedAtomsCol B
fixedAtomsFile kfretBlysAfix.pdb

run 900000

Sorry there is so much info here, I would appreciate help though.

Thanks
Mark

________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Mark M Huntress [markmh_at_bgsu.edu]
Sent: Tuesday, March 02, 2010 10:51 AM
To: ; namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: cell basis vector restart

ah, I was wondering if I should do that, thank you, but the dimensions listed in the xsc file are exactly the same as the ones I started with. But if I measure, in VMD, the dimensions of the .coor output file I am using as the starting coordinates for this run, the box dimensions are bigger than those listed in the xsc file. Is that OK?
Thanks
Mark
________________________________________
From: [linxingyu1986_at_gmail.com]
Sent: Monday, March 01, 2010 10:08 PM
To: Mark M Huntress
Subject: Re: namd-l: cell basis vector restart

read the box vector from the last xsc file when you restart your simualtion

On Tue, Mar 2, 2010 at 6:47 AM, Mark M Huntress <markmh_at_bgsu.edu<mailto:markmh_at_bgsu.edu>> wrote:
Hi, I just did a slow heat, for which I set my cell basis vectors equal to the solvent box dimensions. After the slow heat, the box has increased in size. Do I need to respecify the cell basis vectors to the larger values when restarting?
Thanks

--
Xingyu Lin
Currently:
National Institute of Biological Sciences, Beijing
Dr. Niu Huang's Lab
http://www.nibs.ac.cn/
Tel: 80726688-8572
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427
Postcode: 102206

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