[gmx-users] Need help with tabulated non-bonding potential tablep file

[Justin A. Lemkul]

On 4/23/12 8:54 AM, Marcelo Lopez wrote:
> I get no answer so I insist... ¿Do my questions gets in to the email list?
>

Your messages are arriving on the list.  The documentation for tablep.xvg 
contents is certainly lacking, and unfortunately so too are the threads in the 
archive on the same topic.  Most of them are unanswered or incomplete and thus, 
if you are receiving no reply, we don't know how to offer complete help.

You may have to dive into the code to see how these files are read and utilized. 
  It's not small task, but you'll certainly get your questions answered :)

-Justin

> Hi all: I'm trying to run a coarse grained system with 3 different
> kind of particles, lets call them "A", "B" and "C", and the
> interactions between them are set by means of 3 tabulated potentials
> (not LJ, totally customized ones). I want to introduce 1-4
> interactions with the -tablep optional argument of mdrun. I don't
> understand:
>
> 1) How exactly to write one tablep.xvg file? 3 or 4 values for each
> pair? For example, for the atom indexes 1 and 5, must I write
>
> 1   5   0.0   0.0
> or
> 1    5    0.0
> ?
>
> Or must I write the atom labels?:
>
> A    B    0.0   0.0
>
> 2) Must I put only one tablep.xvg file with all the pairs or must I
> make one separated table for each kind of 1-4 interaction? For
> example:
>
> tablep.xvg (with all the interactions)
>
> or
>
> tablep.xvg, tablep_A_A.xvg, tablep_B_B.xvg, tablep_A_C.xvg, ......
>
> 3) mdrun expects the indexes and 1 or 2 values?
>
> 4) What's the meaning of the value/s at the right of the 2 indexes for
> a not LJ tabulated potential?
>
> 5) The pair interactions are scaled or set to zero when using
> tabulated non-bonding potentials? I need to set them zero...
>
> Thank you in advance.
>
> Johny.

-- 
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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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