From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Sat May 02 2009 - 07:43:34 CDT
namd-l_at_ks.uiuc.edu
Hello everybody,
I am new to namd (switching from AMBER over CHARMM to NAMD) and have a question
regarding the NPAT and NPgT ensemble setup I could not answer myself using
literature (I read so far) and/or Search-engines.
My basic setup for simulating a dual-layer membrane in CHARMM with NPgT/NPAT
ensemble is the following:
NPgT
-----------------------------------
DYNA CPT leap restart nstep 25000 timestep 0.002 -
nprint 100 iprfrq 5000 ntrfrq 5000 iunrea 11 iunwri 12 iuncrd 13 -
iunvel -1 kunit -1 nsavc 500 nsavv 0 -
PCONS pint pref 1.0 pmass 2295 pgamma 20.0 surface tension 30 -
HOOVER reft 303 tmass 2000.0 tbath 303 firstt 303
----------------------------------
and quiet similar the NPAT setup:
---------------------------------
DYNA CPT leap restart nstep 25000 timestep 0.002 -
nprint 100 iprfrq 5000 ntrfrq 5000 iunrea 11 iunwri 12 iuncrd 13 -
iunvel -1 kunit -1 nsavc 500 nsavv 0 -
PCONS pint pref 1.0 pmxx 0. pmyy 0. pmzz 2295 pgamma 20.0 -
HOOVER reft 303 tmass 2000.0 tbath 303 firstt 303
---------------------------------
Now I tried to translate this to namd and ended in the following for NPgT and
for NPAT (for NPAT I just removed "SurfaceTensionTarget" and added
"UseConstantArea yes")
(See end of Mail for namd config)
Now I got three questions:
1) In my CHARMM setup for NPAT (pmxx 0. pmyy 0. pmzz 2295) pmzz is coupling the
box length (z) to the according component of the pressure tensor. Is the keyword
"UseConstantArea" working in the same way? As much as I could see, there is
no option to couple x or y to the according pressure tensor, so I guess NAMD
expects a membrane to be in the X/Y-Plain having the Lipids aligned along the
Z-Axis (Actually the standard setup).
2) Is my namd config for NPAT/NPgT right?
3) Is it more efficient to use "PMEGridSize{X,Y,Z}" (having the factors 2,3 and
5 in mind) then "PMEGridSpacing"? Is "PMEGridSpacing" automatically calculating
the GridSize with respect to the suggested factors?
Thanks for you help
Kind regards
Bjoern
NPgT
---------------------------------
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp 303
langevinHydrogen off
# PBC
cellBasisVector1 51.8459 0. 0.
cellBasisVector2 0. 51.8459 0.
cellBasisVector3 0. 0. 60.
cellOrigin 0. 0. 0.
wrapAll on
# PME
PME yes
PMEGridSpacing 1.0
# Constant Pressure Control
useGroupPressure yes
useFlexibleCell yes
useConstantRatio no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200.
LangevinPistonDecay 100.
LangevinPistonTemp 303
SurfaceTensionTarget 30
---------------------------------
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