Subject: CHARMm pressure.doc

From: "Dr. Richard L. Wood" <[email-masked]>
Date: Fri, 08 Mar 2002 11:58:28 -0500

Hi all

We are still having trouble determing pressures from CHARMm
clacluations.

So we've done a test on a 512 molecule box of water that has a
density of about 1 g/cm^3.  The volume of this box is 15366.93394
Angstroms^3.

I've run a 20 ps Verlet dynamics simulation on thes waters using
periodic boundary conditions.  In the document pressure.doc, I came
across a way to calculate the instantaneous pressures from my
trajectory.

Below is the code I used:
=================================================

SET NTOT = 20

PRES INIT

SET 1 1
LABEL LOOP
  TRAJ READ
     ENER
     PRES INST TEMP 300.0 NDEG 4608 VOLU 15366.9
  INCREMENT 1 BY 1

IF 1 LE @NTOT GOTO LOOP

PRES STAT
=================================================

This outputs the instanteous pressure every ps.  Here's typical output:
==================================================

ENER ENR:  Eval#     ENERgy      Delta-E         GRMS
ENER INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals
IMPRopers
ENER EXTERN:        VDWaals         ELEC       HBONds
ASP         USER
ENER IMAGES:        IMNBvdw       IMELec       IMHBnd       RXNField
EXTElec
 ----------       ---------    ---------    ---------    ---------
---------
ENER>        0  -5242.80489    -26.35422     12.83038
ENER INTERN>        3.61295      0.04294      0.00000      0.00000
0.00000
ENER EXTERN>      496.00280  -4612.07359      0.00000      0.00000
0.00000
ENER IMAGES>       63.63298  -1194.02297      0.00000      0.00000
0.00000
 ----------       ---------    ---------    ---------    ---------
---------

 CHARMM>         PRES INST TEMP 300.0 NDEG 4608 VOLU 15366.9
 -------------------------------------------------------------------------------

 Virial KE       =    -5582.52498               Volume          =
15366.90000
 External Virial =      179.98097               Internal Virial =
3541.70235
 External Virial Tensor  : xx      195.59347 xy       -1.87098 xz
63.70288
                           yx      431.95006 yy      440.08007 yz
-44.40888
                           zx      119.04395 zy     -779.44679 zz
-95.73063
 Internal Virial Tensor  : xx     3422.93484 xy      121.34689 xz
-99.13260
                           yx      121.34689 yy     3836.55309 yz
49.65984
                           zx      -99.13260 zy       49.65984 zz
3365.61912
 External Pressure =     -803.08860           Internal Pressure =
19889.25317
 External Pressure Tensor: xx     -872.75275 xy        8.34845 xz
-284.24702
                           yx    -1927.39358 yy    -1963.67029 yz
198.15574
                           zx     -531.18305 zy     3477.95008 zz
427.15725
 -------------------------------------------------------------------------------

  ======================================================

As can be seen, the internal pressure is 19889.25317 atm, which seems
rather large to me.  The average
for the entire 20 ps run is about 20000 atm.

Now I know the CHARMm units of pressure are in atm, and the volume is in
Angstroms^3.
Is there some kind of conversion or something that I'm missing?  I did a
back of the
envelope calculation and this many waters treated as an ideal gas at 300
K would only
have a pressure of about 1366 atm, which is still large.

Any help will be appreciated!

Richard

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Department of Food Science
120 Stocking Hall
Cornell University, Ithaca, NY 14853