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

[Mark Abraham]

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.

Mark

>
> 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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