AMBER Archive (2005)

Subject: Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 01 2005 - 10:41:08 CST

On Mon, Feb 28, 2005, praveena moldy wrote:
>
> I want to run Poisson-Botzmann MD in NVE ensemble for a small peptide
> Ace-Ala3-NMe with the length of all bonds fixed. I have to
> equilibrate it to 300K slowly within 100ps.The time step of the
> simulaiton which I kept is 1fs. In the first 65ps the molecule is
> made to heat gradually to 300K, and in the successive 25ps the
> temperature is restrained to 300K and no temperature scaling is
> adopted in the successive 10ps.
>
> The input I have used is the one below,
>
> ntt=0,ntc=3,ntf=3,
   ^^^^^

You are setting ntt=0, so that there is no temperature regulation; the
value to temp0 is ignored in this case. Check the temperature profile
of your run. For early simulations, set ntpr to a small value (like 1)
and just run 1000 steps or so, to make sure that things are working the way
you want them to. Then you can attempt longer runs.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu