AMBER Archive (2007)

Subject: Re: AMBER: How to perform MD simulation in NVT ensemble?

From: WANG,YING (wangying_at_ufl.edu)
Date: Thu Aug 23 2007 - 15:53:05 CDT

Hi, GREAT Thanks!!
And I have an additional question........... :) Could I give an
initial velocity of some of the atoms of a protein? Change the
.inpcrd file? And I want to keep this velocity during the whole
NVT simulation process, at the same time, I let the other atoms of
this protein move freely. Is it possible?
Sorry for so many questions................... Thanks very much!!
Thanks the amber community!

On Thu Aug 23 12:18:12 EDT 2007, Thomas Steinbrecher
<steinbrt_at_scripps.edu> wrote:

> Hi,
>
> set ntt>0 (temperature control) and ntb=1 (constant volume) with
> ntp=0 and you have an NVT ensemble. Your systems density needs to
> be equilibrated before that though...
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Thu, 23 Aug 2007, WANG,YING wrote:
>
>> HI, DEAR AMBER MEMBERS,
>> Sorry to bother you! Now I try to perform md simulation of a
>> protein. When I search the manual I only can see the regulation
>> of temperature and pressure. If I try to perform a "constant
>> temperature and volume" dynamics, that is NVT, how can I do?
>> Could you give me some hint? Thanks very much!!
>>
>> Best wishes,
>>
>>
>> --
>> WANG,YING
>>
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>
> 

--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

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