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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 27 16:41:39 CEST 2012

On 28/04/2012 12:19 AM, Marcelo Lopez wrote:
> Thank you very much Mark, I have already in my topology files
> nrexcl = 3
> and
> gen-pairs = no
> Please enlight me... Does this mean that all the 1-4 interactions (I
> have tabulated bonds, angles and dihedrals) are zero?

Look at what the .log file reports for energies (or the .edr file). If 
there are no named 1-4 terms, then there are no 1-4 interactions. grompp 
might report this also. gmxdump on your .tpr does allow you to probe 
this (but not as easily as checking the .log file).

>   Because I'm
> trying to put a strong repulsive part in the non-bonding potentials
> and the energy grows to "Inf".

That may or may not have anything to do with 1-4 interactions, but is 
reasonably likely to be problematic without careful parameterization. 
Also, you haven't said what energy grows without bound, so it's hard to 
know how this relates to the foregoing.


> Thanks.
> 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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