Re: namd question in parameter conversion

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Thu Jan 19 2012 - 02:08:46 CST

Hi Liqun,

I think there should be normal and decent parameters for pairlist distance
and switch distance. Too large or too small distance would cause
misordering. But it should be also case to case considered. It also largely
depends on the environment of the system.

Best,
Boyang

On Thu, Jan 19, 2012 at 12:27 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,

-- 
Boyang Wang, Ph.D.

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