Re: [AMBER] remd

From: Daniel Roe <>
Date: Thu, 19 Jun 2014 14:57:09 -0600


Remember, the tutorials are designed only to give a brief introduction make
people familiar with the given technique(s). They should not be taken as
"this is the only way to do something". That said, there are several
reasons why you might want a new velocity distribution, the foremost of
which is if you want two or more independent runs from the same set of
starting coordinates.

Hope this helps,


On Wed, Jun 18, 2014 at 6:35 PM, whb <> wrote:

> Hi all:
> When I was reading the turotial of
> remd(, I found a question
> that the author set up irest=0, ntx=1 rather than irest=1,ntx=5 in the
> remd.mdin. I want to know why we give up the speed produced by the
> equilibrium step and produce a new speed by ntx=1.
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 19 2014 - 14:00:02 PDT
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