Re: [AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD

From: Ross Walker <>
Date: Thu, 20 Oct 2011 00:32:00 -0700

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

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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Oct 20 2011 - 01:00:02 PDT
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