Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Aug 02 2007 - 14:42:37 CDT

What do you mean "output for VDW, etc."?

Electrostatics are calculated using the charges in the PSF file and
Coulomb's law ( F = k q1*q2/r^2 ).

On Aug 2, 2007, at 10:29 AM, Sathish Gurupatham wrote:

> hi Gumbart,
>
> my aim is just to simulate a water molecule at 310k.
> i did it but am not getting any output for VDW,Electrostatic
> potentials.(i got it for bond,angle potentials)
> I hope, for VDW potential the expression is given in parameter
> file,but for electrostatic potential where do we give the expression?
> the belowmentioned is the parameter file i have applied.
> pls help me if i am wrong anywhere.
> thanks ,
> sathish.
>
> BONDS
>
> !V(bond) = Kb(b - b0)**2
>
>
>
> !atom type Kb b0
>
> H OH2 450.000 0.9572
>
>
> ANGLES
>
>
> !V(angle) = Ktheta(Theta - Theta0)**2
>
>
> !atom types Ktheta Theta0 !Kub !S0
>
> H OH2 H 55.000 104.52 !35.00 !2.41620
>
>
>
> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
>
> !atom ignored epsilon Rmin/2
>
>
> H 0.000000 -0.9510000 1.000000
> OH2 0.000000 -0.7100000 1.000000
> END
>
>
> JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Your question is very vague and confusing. Have you done the VMD
> and NAMD tutorials yet? The appendices in the NAMD tutorial
> discussing the different file types (including the parameter file)
> will be particularly helpful.
>
> All you need to simulate a water box is the VMD solvate plugin, a
> simple configuration file (can be adapted from the NAMD tutorial)
> and any of the standard parameter files, such as the one included
> with the NAMD tutorial. Also, you may find the water case study
> (on our website) interesting.
>
>
> On Jul 31, 2007, at 11:09 AM, Sathish Gurupatham wrote:
>
>> hi all,
>> i am simulating water molecule to understand namd.
>> i got some o/p but i know its wrong.
>> where can i have the para,conf files for a water molecule?
>> pls help me.
>> thanks.
>>
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