Re: namd question in parameter conversion

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Jan 18 2012 - 12:35:01 CST

I may be wrong, but as the pairlist is the list of atoms that are within
the cutoff range, I think the general convention is to have pairlist be
larger than cutoff, perhaps by 2 angstroms or so, such that the pairlist
being used for the non-bonded cutoff is always at least mostly accurate.

~Aron

On Wed, Jan 18, 2012 at 11:27 AM, Liqun Zhang <lxz79_at_case.edu> wrote:

> Dear namd users:
>
> I like to convert the system from charmm into namd. I used following
> command in charmm:
>
> nbonds atom cdie cutnb 16.0 ctofnb 12.0 ctonnb 10.0 bycb -
> wmin 1.0 eps 1.0 inbfrq -1 cutim 16.0 imgfrq -1 -
> ewald pme order 6 spline kappa 0.34 fftx @fftx ffty @ffty fftz @fftz
>
> which means that i used the cufoff of van der waal interaction at 16 A,
> the switching value is 12 A, and the smoothing function begins at 10 A.
>
> In the namd simulations, I like to use the same kind of parameters in NPT
> simulation, I have following content in the input file:
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 16.
> switching on
> switchdist 12.
> pairlistdist 14
>
> here, I am not sure how to fill the pairlistdist value based on charmm
> parameters, and I believe the cutoff setting, switchdist setting should be
> correct. Can somebody help me on this? Thank you very much.
>
> Kindly regards,

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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