AMBER Archive (2004)

Subject: Re: AMBER: non-isotropic pressure scaling

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Wed Apr 14 2004 - 07:48:59 CDT

bob,

finally i compiled pmemd with the ntp=2 support. i'd like now to test
it. you recommended to me dhfr benchmark. however it is equilibration
with ntp=0, so i want to check what to do next:

should i
1) change ntp=0 to ntp=2 in bench.dhfr, run with classical sander7
2) change execution parameters in bench.dhfr
3) add some parameters to mdin section in bench.dhfr to test all modes
(cit / nocit)
4) execute with pmemd
5) compare the outputs

is it so, or am i missing something? what differences should i look for
and what are reasonable values?

regards,
lubos 

-- 
Lubos
_@_"
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