[gmx-users] rlist and rcoulomb

[Swarnendu Tripathi]

Hello,

Thanks for the reply.

So, can I think that when I set rcoulomb > rlist then the Coulomb (LR)
energy term is providing some kind of correction over the Coulomb (SR)
energy term.

-Swarnendu

On Thu, Oct 21, 2010 at 4:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Swarnendu Tripathi wrote:
>
>> Dear gromacs users,
>>
>> In section 4.6.3 of gromacs 4 manual it says ``... the interactions
>> between pairs that do not fall within rlist but do fall within
>> max(rcoulomb,rvdw) are computed during neighbor search (NS), and the forces
>> and energy are stored separately, and added to short-range forces at every
>> time step between successive NS.''
>>
>> Now I find that if I use rlist (= rvdw) = rcoulomb then I only have
>> Coulomb (SR) values in the md.log file but if I use rlist (= rvdw) <
>> rcoulomb then I get both Coulomb (SR) and Coulomb (LR) values in the md.log.
>> In both cases I have assigned vdwtype=user and also rcoulomb=user for a
>> tabulated potential that I use.
>> Now, my question is how in the second case when rlist < rcoulomb I am
>> getting the Coulomb (LR) values in md.log? Particularly, I want to know
>>
>
> You have twin-range interactions.  Some interactions do not occur within
> rlist, but occur within rcoulomb, which is beyond rlist.  This is exactly
> the case stated in the manual.  If rlist = rvdw, then max(rvdw,rcoulomb)
> finds that rcoulomb is larger than rvdw and thus defines the outer bound of
> the twin-range setup.
>
>
>  how the Coulomb (LR) is calculated? Is it calculated in the same way as
>> Coulomb (SR) and simply denoted as  Coulomb (LR), since rlist <
>>
>
> Probably in the same was as Coulomb (SR), but with the frequency described
> in the manual.
>
>
>  rcoulomb? Or, in this case it is suggested that I should always use
>> rlist=rcoulomb.
>>
>>
> Using rlist=rcoulomb is fairly common for many force fields, but whether or
> not this is required for your model is up to you.
>
> -Justin
>
>
>  Any suggestion is appreciated and thanks in advance.
>>
>> -Swarnendu
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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