VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Oct 25 2018 - 18:35:17 CDT

Ahh! Looking at this with fresh eyes, I didn't intend to disparage the effectiveness of the barostats. They do totally work on longer time scales. It is just that if you compare them against typical thermostats, where the fluctuations around the target are tiny, there is some confusion as to why the instantaneous pressure isn't stable. That is what the conservation talk was about.

-Josh

On 2018-10-25 12:58:48-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

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/Drh8UhlGJ2ANxoi8s0%26m%3DXlIfhOyxGysKFVyjm3-hpDtMV5cQlXZtMbSNtT6IbP8%26s%3DyCfc3zgaa7jP3KfH2w86y45ZotJniL5BzczRscHtSBQ%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C3828f55ec5a04e6f264a08d63aabe371%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636760907276196697&sdata=Z3%2F%2FAS1PSaLRQMQIftVTErrKsHhBCq4gGwx2lHm%2BRzw%3D&reserved=0>
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