Hi Ross,
Thank you very much for the extensive explanation!
Best,
Mo
On Thu, Oct 20, 2011 at 3:32 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mo,
>
> > May I ask how the "cut" functions in PMEMD facility? I have learned
> > that
> > while running MD using CHARMM, we could specify ctonnb, ctofnb, so that
> > the
> > switching function is turned on at the distance < ctofnb and > ctonnb
> > in
> > calculating vdw energy, as well as the shifting is turned on in
> > calculating
> > electrostatic energy. On the other hand, in Amber, I found we could
>
> AMBER traditionally has just used a single cut off value. The equivalent of
> ctonnb and cutnb to Charmm for the electrostatic calculation are determined
> automatically so there is no need to set them. There is no shifting for PME
> runs and erfc is used to partition between direct and reciprocal space so
> there is no need for a switching function.
>
> For VDW AMBER (sander and pmemd) uses a strict truncation at the cutoff,
> with no switching function. A long range correction is given by default and
> for the majority of simulations this is sufficient.
>
> > define
> > CUT, or vdw_cutoff & es_cutoff when using PMEMD, in which CUT
> > represents the
> > cutoff value. May I ask if the CUT in PMEMD is the same as ctofnb in
> > CHARMM?
>
> PMEMD lets you define either 'cut' which applies to both the EEL direct
> space sum and VDW cutoffs or specify both vdw_cutoff and es_cutoff. In the
> later case it is possible, for example, to use a larger cutoff for the VDW,
> say 10 angstroms, and a smaller cutoff for the electrostatics, say 8
> angstroms. This works because PME calculations deal with the long range
> electrostatics beyond the es_cutoff. I believe cut, vdw_cutoff and
> es_cutoff
> are all logically equivalent to CTOFNB in charmm given the restriction that
> CTOFNB == CTONNB. CUTNB is equivalent to cut + skinnb. Although skinnb is
> effectively a performance tuning parameter which in the case of pmemd is
> optimized automatically by the code.
>
> > And is there a similar parameter of ctonnb in PMEMD? And if so how is
> > it
> > defined? The parameter RGBMAX is set to be 25 as default? May I ask if
> > this
> > is also related to any CHARMM parameter? Finally, may I ask what is the
>
> RGBMAX is related just to implicit solvent GB calculations. It is ignored
> in
> PME calculations. It defines the cutoff when determining effective radii. I
> have not looked closely at the GB models in charmm to determine what this
> would be logically equivalent to. It maybe what is CUTalpha in charmm but
> that's a guess.
>
> > name
> > of the source code file that contain all these parameters? Thank you
> > very
> > much!
>
> Do you mean the default parameters? See
> $AMBERHOME/src/pmemd/mdin_ctrl_dat.fpp - this contains the code for reading
> the ctrl namelist and also sets all the defaults.
>
> 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 Thu Oct 20 2011 - 09:30:04 PDT
