---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, Jan 31, 2013 at 1:03 PM
Subject: Sampling of a point by a molecule while keeping the relative
position of the molecule unchanged in TMD
To: AMBER Mailing List <amber.ambermd.org>
Hi all,
I have some CO2 molecules placed at particular , pre-determined points
inside a protein. I want to sample the positions of CO2 molecules around
those particular points while keeping their relative position with respect
to the surrounding of each CO2 as constant as possible. When I went through
the description of the technique in the AMBER manual I thought targeted MD
would serve the purpose coz it allows to give a set of atoms as a reference
and restrain the motion of the atoms, in terms of RMSD while the simulation
is going on.
Letz say that the residue numbers that I use as surrounding for a
particular CO2 are 410, 385, 835, 525 and the residue number of the
particular CO2 is 902
If I have an mdin file like below, will it serve my purpose(i.e to keep the
position of the residue 902 more or less constant with respect to the
surrounding while having my initial protein.prmcrd file as the reference in
*-ref*)?
TMD
&cntrl
ntx=1,irest=0,
nsnb=1,ntpr=5,ntwx=100,nstlim=500000,dt=0.001,
ntc=2,ntf=2,ntb=1,iwrap=1,
ntt=3,temp0=300,tempi=300,gamma_ln=4,ig=10502,
cut=8.0,
igtmd=1,tgtfitmask=':410,385,835,525,902',
tgtrmsmask=':410,385,835,525,902', tgtrmsd=0.0, tgtmdfrc=1.0,
/
Please suggest if any modifications are required. And about the force
constant(tgtmdfrc=1.0), should I apply a higher force constant? If so like
how much?
Thank you very much
Sajeewa Dewage
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Received on Thu Jan 31 2013 - 13:30:03 PST
