VMD-L Mailing List

From: Gumbart, James C (gumbart_at_physics.gatech.edu)
Date: Thu Oct 25 2018 - 12:53:03 CDT

The pressure is known to fluctuate significantly, but the algorithm is reliable. I think there are a lot of older posts on the NAMD mailing list discussing this.

Best,
JC

On Oct 23, 2018, at 10:26 AM, Norge Cruz Hernández <norge_at_us.es<mailto:norge_at_us.es>> wrote:


Hi,

I am performing an NPT simulation of the following molecular system:

- protein ( 26400 atoms)

- waters ( 9250 TIP3 molecules)

I am including in the conf file:

# Integrator and dynamics parameters

timestep 1.0

#Periodic boundary conditions
cellBasisVector1 106.936 0.0 0.0
cellBasisVector2 0.0 108.170 0.0
cellBasisVector3 0.0 0.0 107.205
cellOrigin 125.483 128.736 35.117
wrapWater on
wrapAll on

#Electrostatics with PME
PME yes
PMEGridSpacing 1.0

# Integrator and dynamics parameters
rigidTolerance 1.0e-8
timestep 1.0
switching on
switchdist 10.
cutoff 12
pairlistdist 14
stepspercycle 10
exclude scaled1-4
1-4scaling 1.0
zeromomentum on
watermodel tip3
fullElectFrequency 1

# Constant Temperature Control is off
langevin on
langevinDamping 1.0
langevinTemp 300
langevinHydrogen no

#Constant Pressure Control
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 50
langevinPistonDecay 25
langevinPistonTemp 300
useGroupPressure yes
useFlexibleCell no
useConstantArea no

# Run simulation
minimize 1000
reinitvels 300
run 5000000

After 1000 steps I have:
TOTAL: -375602.3323
TEMP: 0.0000
PRESSURE: -6730.7901
PRESSAVG: -6730.7901

Just starting the run of the dynamic, I have at step 1000:
TOTAL: -273329.7246
TEMP: 298.5816
PRESSURE: -2909.3038
PRESSAVG: -2909.3038

So, the temperature takes value of 172.4638, and it changes gradually up to 300. After 18000 I have a temperature around 195-198, which is not bad.

However, after 88000 steps I have:
TOTAL: -203037.5677
TEMP: 297.5823
PRESSURE: 87.7274
PRESSAVG: -1.0424

after 99600 steps I have:
TOTAL: -203200.5834
TEMP: 297.7877
PRESSURE: -383.3437
PRESSAVG: 3.5970

It is, the PRESSURE changes a lot step by step....
So, why do I not obtain a value of PRESSURE close to 1.01325?
Do I have to change/include some parameters in the conf file to get a value around 1.01325 for PRESSURE?

Thanks!!!
--
Prof. Norge Cruz Hernández
Dpto. Física Aplicada I
Escuela Politécnica Superior
Universidad de Sevilla
calle: Virgen de África 7,
Sevilla, Spain, E-41011
Phone number:
+34 - 954 55 01 67
+34 - 954 55 99 70
Fax number:
+34 - 954 55 43 41
Web: http://personal.us.es/norge/jP3KfH2w86y45ZotJniL5BzczRscHtSBQ&e=>
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