AMBER Archive (2003)

Subject: Re: non-periodic system

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed May 21 2003 - 21:47:34 CDT

Hi,

Ok, so I've generated in amber a box with a solvated peptide. Then I turn
on amber in NAMD but I impose cylindrical harmonic boundary conditions (I
do not know how to generate a cylindrical system so that's why I decided
to try to generate a box and by defining the cylindrical BC to select only
the part I want to "observe"). I then use Berendsen T and P coupling.
I can not use PME for the electrostatic so I turn it off (NAMD complains
about using it).
The way I understand it is that using cylindrical boundary conditions these
are non-periodic, thus NPT should not work (unless there is a periodicity
on the cylinder axis but then there is the problem on the other two axis).
If NPT works and this means that imposing the cylindrical boundary
conditions preserves periodicity I do not know how that is taken into
account ( I can not imagine cylindrical periodic boundary conditions).

Basically I am trying to understand why my run DID work.

And why not, maybe one day someone will come up with a brilliant idea
(that would sound paradoxical) to run NPT for nonperiodic systems :)

Thank you,
Ioana

***********

Here is my NAMD configuration file.

#Configuration file for NAMD, NVT run trying to heat up a water box
#from 0K to 300K

# initial config
exclude scaled1-4
1-4scaling 0.8333 #=1/1.2 from Amber
scnb 2.0 #this is for the van der waals
amber on
parmfile ./pepsolvK.prmtop
coordinates ./water_heat.coor
velocities ./water_heat.vel
seed 314159

restartfreq 100
outputEnergies 10
outputTiming 100
xstFreq 100
dcdFreq 50
outputname TPCyl
restartname TPCyl.restrt
binaryrestart no
binaryoutput no
DCDfile TPCyl.dcd
COMmotion no
wrapAll on
wrapNearest on

switching on
switchdist 9.5
cutoff 10.0
pairlistdist 15.0

#Amber uses rigid water and SHAKE H-bonds.
rigidBonds all

timestep 2
nonBondedFreq 1
fullElectFrequency 1
stepsPerCycle 1

#constant temperature simulation using Berendsen Temp coupling
tCouple on
tCoupleTemp 300
tCoupleFile ./water_Tcouple.pdb
tCoupleCol B

#constant pressure simulation using Berendsen Pressure coupling
berendsenPressure on
berendsenPressureTarget 1.01325
berendsenPressureCompressibility 4.9e-5
berendsenPressureRelaxationTime 500
berendsenPressureFreq 1

# periodic cell
#cellBasisVector1 39.8234 00.00 00.00
#cellBasisVector2 00.00 39.1324 00.00
#cellBasisVector3 00.00 00.00 33.0094
#cellOrigin 19.9117 19.5662 16.5047

#trying to use Cylindrical harmonic BC
cylindricalBC on
cylindricalBCCenter 19.92 19.58 16.40
cylindricalBCAxis x
cylindricalBCr1 15.0
cylindricalBCl1 39.0
cylindricalBCk1 1.0
cylindricalBCexp1 2

#fix the peptide atoms
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fixpep.pdb
fixedAtomsCol B

#pressure control with SHAKE
useGroupPressure yes
useFlexibleCell yes
useConstantRatio yes

# protocol params
numsteps 10000

On Wed, 21 May 2003, Michael Crowley wrote:

> Dear Ioana,
> I am curious to know what the meaning of pressure is
> in a non-periodic system. How does one model the "pressure"
> in a non-periodic system? Where is the external (constant)
> pressure coming from?
> What is the non-periodic NPT model in NAMD?
>
> THanks
> Mike
>
> -----------------------------------------------------------------
> Physical mail: Dr. Michael F. Crowley
> Department of Molecular Biology, TPC6
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, California 92037
>
> Electronic mail: crowley_at_scripps.edu
> Telephone: 858/784-9290
> Fax: 858/784-8688
> -----------------------------------------------------------------
>
>
>
>