Hi Homa,
> I have a question about AMBER. I want to do MD for about 10 ns, after 2
> ns my system reaches to equilibrate state, during this time I used
> NTT=3, should I change the Termostate to NTT=1 for the rest of the
> simulations
It depends on what you are ultimately looking at. From a pure performance
perspective you will get better performance if you are running in parallel
using ntt=1 than you will using ntt=3 (without some undocumented compile
time 'hacks') so you might want to switch to ntt=1 for that. You might also
want to consider turning off the thermostat entirely. Set tol and dsum_tol
and order of magnitude tighter than the defaults, ntb=1 and ntt=0 and you
should be good to run NVE. This will also give you the best performance.
However, there is equally nothing wrong with just continuing with ntt=3 as
long as you are not looking at certain things such as correlation functions
etc which might be influenced by the presence of a thermostat. One thing to
consider, if you do switch to ntt=1 it is probably best to use a very weak
coupling (tautp=10.0 or greater). This starts to approximate NVE the larger
you make it.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Sun May 09 2010 - 19:30:04 PDT
