RE: AMBER: Temperature equilibration

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 29 Aug 2005 08:44:08 -0700

Dear Anthony,

> I have a question, for example if I want to run a 3ns
> simulation and I set the
> tempi=0.0 and temp0=300 how much time of the 3ns will be use
> for system
> equilibration??? Is preferable to equilibrate the temperature
> of the system
> with restrain???

In the example you give it would get to 300K very quickly. Roughly in line
with the value of tautp (ntt=1) or in relation to the size of gamma_ln
(ntt=3). Typically this will be within 5 or 10ps or so.

Ideally if your system is quite large and explicit solvent it is advisable
to heat slowly using weight restraints. E.g.

ntt=1,dt=0.002, nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=100000,
                  value1=0.1, value2=300.0, /
&wt type='END' /

This will heat the system linearly from 0.1K to 300K over 200ps.

I hope this helps
All the best
Ross



/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be ready every day, and should not be used for urgent or sensitive issues.


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Aug 29 2005 - 16:53:00 PDT
Custom Search