[gmx-users] How to use -tablep mdrun option?

Marcelo Lopez shonytolengo at gmail.com
Fri Apr 27 16:19:08 CEST 2012

Thank you very much Mark, I have already in my topology files

nrexcl = 3


gen-pairs = no

Please enlight me... Does this mean that all the 1-4 interactions (I
have tabulated bonds, angles and dihedrals) are zero? Because I'm
trying to put a strong repulsive part in the non-bonding potentials
and the energy grows to "Inf".


Marcelo Lopez

El día 27 de abril de 2012 10:38, Mark Abraham
<Mark.Abraham at anu.edu.au> escribió:
> On 27/04/2012 11:07 PM, Marcelo Lopez wrote:
>> Hi all,
>> I'm trying to run a coarse grained system with tabulated non-bonding
>> potentials for 3 kind of particles. I need to set all the 1-4
>> interactions to zero
> Why not use nrexcl = 3 in your [moleculetype] like the example in manual
> 5.7.1? (and probably gen-pairs = no for your force field)
>>  but I can't find in the manual or elsewhere hot
>> to construct the tables for the -tablep option of mdrun.
> Searching the manual text for "tablep" finds me information in section 7.3,
> which strongly suggests the information in 6.7.2 is applicable.
>> I've readed a thread in the mailing list but still the information I
>> get is uncomplete... (the manual says absolutely NOTHING!)
>> 1) In these tables, do I specify the index number of every 1-4 pair or
>> only the labes of the groups involved? Followed by the C6 and C12
>> parameters.
> Only a functional form is specified in the table. Topology (which 1-4 pairs
> exist) is entered in the .top file. Parameters (charge, C6 and C12)
> likewise. Go and look at 6.7.2 and the example tables in your GROMACS
> distribution.
>> For example, for the atom index 1 and 5 (energy groups A and B), one
>> tablep*.xvg file must contain this
>> 1   5   0.0   0.0
>> or this (valid for all the AB 1-4 pairs?)?
>> A    B    0.0    0.0
>> I ask... And still something is missing?
>> The system has no charges, do I say this too in every  tablep*.xvg file?
>> how?
> Charges are specified in the [atoms] section of your [moleculetype]. If
> they're zero, then nothing will ever be computed from them, so you can
> probably use anything you like with the the f() part of the tabulated
> potentials.
> Mark
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