AMBER Archive (2003)

Subject: Re: AMBER: Pressure during MD

From: David A. Case (case_at_scripps.edu)
Date: Sun Nov 16 2003 - 16:52:36 CST

On Sun, Nov 16, 2003, Joo Barroso wrote:
>
> I'm rather new with Amber, so I have a simple question regarding the
> pressure of the system during MD. I'm using Amber 7 and a periodic system
> at 300 K. I'm running first equilibration at constant volume (ntb=1 and
> ntp=0), and I change to constant pressure for the MD (ntb=2 and ntp=1). I
> didn't give any value for "press0", assuming that it would be the default
> value of 1 atm. However, in each step the output file reads press=0.0 both
> in equilibration and the remaining simulation (see example below). Should I
> be concerned about this? Is the system running at 1 atm or do I have to
> specify the pressure in the input file?
>
> NSTEP =1365000 TIME(PS) = 1365.000 TEMP(K) = 299.63 PRESS = 0.0
> Etot = -63273.9308 EKtot = 26416.5302 EPtot = -89690.4610
> BOND = 15843.0623 ANGLE = 3334.9801 DIHED = 2305.3420
> 1-4 NB = 1430.4541 1-4 EEL = 10987.8157 VDWAALS = 11638.1704
> EELEC = -135230.2857 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.2029E-04
> ------------------------------------------------------------------------------

It really doesn't look like you are doing a constant pressure simulation.
Double-check the mdout file to be sure that ntb=2 and ntp=1. The default
pressure is indeed one atmosphere, but you are somehow not getting a pressure
calculation. Without seeing more about your input or output, I cannot say
why.

..regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu