amber-developers: SHAKE and Thermodynamic Integration

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Fri, 14 Sep 2007 22:41:31 -0400 (EDT)

Dear All,

I have a question about the SHAKE algorithm. Here is the input file I am
using:

------ md.in ------------------------------------
1 ns simulation with lambda = 0.1 - Production
 &cntrl
  imin=0,
  ntx=1,irest=0,
  ntpr=50,ntwr=1000,ntwx=1000,
  ntc=2,ntf=2,ntb=1,cut=8,
  noshakemask = '.%DH | (:4,12.H6) | (:4,12.%H)',
  ntr=0,
  nstlim=1000000,dt=0.001,nscm=5000,nrespa=1,
  ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
  ntp=0,taup=2.0,pres0=1,
  icfe=2,klambda=6,clambda=0.1
 /
-------------------------------------------------

Shake option is selected; and noshakemask is used. When I look at the .out
file; I see the following: 

----
Noshake mask .%DH | (:4,12.H6) | (:4,12.%H); matches     4 atoms
   Removing shake constraints from N6   RA     4 -- H61  RA     4
   Removing shake constraints from N6   RA     4 -- H62  RA     4
   Removing shake constraints from N6   RA    12 -- H61  RA    12
   Removing shake constraints from N6   RA    12 -- H62  RA    12
   Setting ntf to 1
----
Noshakemask is removing only 4 atoms' shake constraint. H6 atom and DH
type dummy atoms are used in the final states.
My question is this: How does SHAKE algorithm work in Thermodynamic
Integration Approach? When SHAKE and noshakemask is used, does it apply
these constraints on initial state? (And as a result, the atoms on the
final state corresponding to these constrained atoms are SHAKEN, too?)
I thought that when shake and noshakemask is defined in the input file,
the constraints will be applied on both states explicitly (for instance, I
was expecting the above sander output file to show not just 4 atoms, but
10 atoms). Thanks.
Best,
-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------
Received on Sun Sep 16 2007 - 06:07:46 PDT
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