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Regarding the parameters in the MC simulation
#28321 09/15/11 11:11 AM
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Ramya Offline OP
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I tried MC simulation with the following parameters for the peptide
! Single atom moves for the peptide atoms
MOVE ADD MVTP CART WEIGht 25.0 DMAX 70.0 -
ARMP 0.40 ARMA 0.4 ARMB 0.4 DOMCf 5.0 ANISotropic 0 LABEL SING -
SELE (.NOT. RESNAME TIP3) END

! phi dihedral angle rotations
MOVE ADD MVTP RROT BYREsidue WEIGht 6.5 DMAX 95.0 LABEl PHI -
ARMP 0.45 ARMA 0.4 ARMB 0.4 DOMCf 10.0 FEWEr 1 -
SELE TYPE N END SELE TYPE CA END

! psi dihedral angle rotations
MOVE ADD MVTP RROT BYREsidue WEIGht 6.5 DMAX 95.0 LABEl PSI -
ARMP 0.45 ARMA 0.4 ARMB 0.4 DOMCf 10.0 FEWEr 1 -
SELE TYPE CA END SELE TYPE C END

! omega dihedral angle rotations
MOVE ADD MVTP TORS WEIGht 6.5 DMAX 95.0 LABEl OMEG -
ARMP 0.45 ARMA 0.4 ARMB 0.4 DOMCf 9.5 FEWEr 1 -
SELE TYPE C END SELE TYPE N END

! Individual rotation of the peptide torsions
MOVE ADD MVTP RROT BYREsidue WEIGht 6.5 DMAX 95.0 FEWEr 1 LABEL PDIHE -
ARMP 0.45 ARMA 0.4 ARMB 0.4 DOMCf 9.5 -
SELE ALL END

Is it correct to set the value of DMAX as 70.0 for the cartesian translation and DMAX as 95 for the torsion?
I used these values as the simulation was run by using it.
Does DMAX means the initial maximum displacement for each move or the entire maximum move allowed?

Thanks for any comments/suggestions.


Ramya.L.
Re: Regarding the parameters in the MC simulation
Ramya #28322 09/15/11 05:58 PM
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rmv Online Content
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You have to evaluate the effectiveness of the DMAX choices based on the sampling results, including the acceptance ratio. Those DMAX values are markedly higher than the examples in mc.doc and the MC testcases, and could lead to a low acceptance ratio. The complexity and density of the system will have an impact on the best choices for DMAX.


Rick Venable
computational chemist

Re: Regarding the parameters in the MC simulation
rmv #28324 09/16/11 10:43 AM
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Ramya Offline OP
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Thank you Rick, for the reply.


Ramya.L.

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