Hi Mo,
> May I ask in what way do the wrong scee and scnb affect the dynamics? I
> have
> compared the decomposed energy terms calculated from Amber (setting cut
> = 8)
> as well as CHARMM (using pmewald and vdw atom vswitched by setting
> ctonnb =
> 8, ctofnb =8 and cutnb =12), and the decomposed potential energy terms
> are
> basically the same. So I wonder how scee and scnb in amber PMEMD affect
> the
> dynamics. Do they affect the random forces in langevin dynamics? I
> wonder if
> my previous simulation should be trashed since I used the older version
> and
> did not use the default values of scee and scnb. Thank you very much!
The SCEE and SCNB values are divisors for the 1-4 electrostatic and nonbond
forces. That is the direct space sum is:
EEL = (q[i]*q[j])/r[ij] where i is not bonded to j and i does not make an
angle with j. In the case of I being involved in a 1-4 interaction with j
(i.e. they form a dihedral) then the EEL for ij is EEL[ij]/scee. Similar
rules apply for the VDW term. This means that if you set scee and scnb to
the incorrect values for the force field you are using then essentially ALL
of your dihedral terms will be incorrect since the dihedral is actually the
sum over Cosine terms making up the dihedral plus the scaled EEL and VDW
interactions.
Since the tertiary structure is effectively determined by the subtleties of
the dihedrals so running with the wrong SCEE and SCNB values will have a
profound effect on the dynamics of your protein.
Note the CHARMM force field does not scale 1-4 EEL interactions and the
variation in 1-4 SCNB interactions is actually handled by having different A
and B coefficients for 1-4 VDW terms than for regular VDW interactions.
Hence the equivalent of the SCEE and SCNB settings do not appear in Charmm.
In short. Yes throw the original simulations run with the wrong SCEE and
SCNB values away and run them again.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Oct 21 2011 - 21:30:03 PDT
