Re: AMBER: temperature does not reach to temp0

From: David A. Case <case.scripps.edu>
Date: Tue, 19 Aug 2003 08:47:15 -0700

On Tue, Aug 19, 2003, Majid moghaddam wrote:

> I am trying to do MD simulations on a peptide in
> water(TIP3P modell) by amber7. I did energy
> minimization 1000 steps steepest descent method, then
> started equilibration in constant volume using bellow
> input parameters:
>
> imin=0, ntb=1, ntc=2, nstlim=100000, cut=12.0,
> dt=0.002, ntx=1, irest=0, ntt=0, tempi=250, temp0=300,
                            ^^^^^
>
> I expected temperature to reach 300 but it did not.

ntt=0 means "do not do any temperature regulation"...the system will do
whatever Newton's equations tell it to, and temp0 is ignored. You probably
want to set ntt=1.

...good luck..dac 

-- 
==================================================================
David A. Case                     |  e-mail:      case.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.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Aug 19 2003 - 16:53:01 PDT
Custom Search