AMBER Archive (2004)

Subject: Re: AMBER: non-isotropic pressure scaling

From: David A. Case (
Date: Wed Apr 14 2004 - 10:36:52 CDT

On Wed, Apr 14, 2004, Lubos Vrbka wrote:
> 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

Bob Duke is out of e-mail contact for a while, but the above strategy sounds
like a good one: basically, you want to assure yourself that pmemd and sander
are giving equivalent results with ntp=2. Step 3 is probably not really
necessary; test pmemd with the paths (presumably cit) that you really plan to

...good luck....dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to