[gmx-users] About coulmb & Vanderrwalls cutoff

[Justin Lemkul]

On 6/4/13 9:48 PM, vidhya sankar wrote:
> Dear Justin  Thank you for your Previous reply.
>                                                                               As yo mailed me  The Defaut      Value for vandewalls and Electrostatics  in GROMOS96 53A6  is  PME option
> s_type     = grid
>   nstlist     = 5
>   rlist       = 0.9
>   rcoulomb    = 0.9
>   rvdw        = 1.4
> But in          you  Umbrella sampling you are using    GROMOS96 53A6 FF there you quoted  different  Parameters  in your em.mdp file
>
>
> nstlist     = 1         ; Frequency to update the neighbor list and long range forces
> ns_type     = grid      ; Method to determine neighbor list (simple, grid)
> rlist       = 1.4       ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME       ; Treatment of long range electrostatic interactions
> rcoulomb    = 1.4       ; Short-range electrostatic cut-off
> rvdw        = 1.4       ; Short-range Van der Waals cut-off
> pbc         = xyz
>
> can i Take 1.4 instead of 0.9 value

The value of rcoulomb is a bit more flexible when using PME, but unless you have 
a basis for changing it (and having demonstrated that the change is harmless), 
you shouldn't deviate from the parameters given for the force field.

> oterwise is there is Any spcification according to system and BOx size

The contents of the system and size of the box do not dictate the parameters 
that are set; the force field does.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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