Re: [AMBER] How to define NO SHAKE

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 2 Jul 2013 08:18:00 -0600

Hi,

The 'noshakemask' variable has the same format as other namelist
variables (var = <value>,) so try:

ntc = 2, noshakemask = '.12230,12245',

See section 'C. ambmask' in the Amber 12 manual for more details on
mask selection syntax.

Hope this helps,

-Dan

On Tue, Jul 2, 2013 at 6:28 AM, Sindrila Dutta banik
<sindrila.duttabanik.yahoo.com> wrote:
> Dear All,
>
> I am simulating a protein system using SHAKE algorithm for the bonds which involve H atom (using ntc = 2). Now I want to exclude a bond between 12230 and12245 (involve H atom) from this SHAKE. As I understood from the manual that I have to use "noshakemask" for this. But I could not understand how to apply this in the input. Like the following way-
>
> ntc=2 .12230 @12245
>
> With best regards
>
> Sindrila
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 02 2013 - 07:30:03 PDT
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