[gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 7 03:17:41 CEST 2012

On 7/05/2012 5:50 AM, Marcelo Lopez wrote:
> For sure, this wouldn't happened if the information to run all the
> Gromacs features were clearly explained in the place where should be:
> the manual.

Life would be good if everything was perfect, but when you're relying on 
free software provided by largely volunteer effort, you have to accept 
some imperfections.

> Next time save some words and use your time to do a better
> documentation job... unless you're trying to have some advantage...

You started these requests by asserting that no documentation existed. 
So various people who might have helped you were probably annoyed and 
decided not to give time to you. However, you got pointed to a likely 
source of information. You seem to have ignored that. Eventually I got 
bored of ignoring your repeated requests and pointed you in the right 
direction again. Others have made worthwhile suggestions, but as far as 
we know you're ignoring them, too. Your frustration with solving your 
problem is understandable, but your assumption that you are entitled to 
perfect free software and to abuse those who help produce it is not 


> Cheers!
> 2012/5/5 Mark Abraham<Mark.Abraham at anu.edu.au>:
>> On 5/05/2012 11:39 PM, Marcelo Lopez wrote:
>>> Hi, all, I'm still confused about how to set up 1-4 interaction tables
>>> for tabulated non-bonding potentials when using the -tablep option in
>>> mdrun.
>>> The specific question is:
>>> How must I specify the 1-4 interaction in those tables? How many
>>> columns and with what?
>> I suggested places to look for this information in answer to this question
>> more than a week ago.
>> http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html Your
>> reply addressed only another part of the discussion. Why are you asking the
>> same question again without appearing to have used the help you've been
>> given?
>>> My primary goal is to set all the 1-4 interactions equal to zero. I
>>> have some 1-4 pairs that aren't involved in dihedrals, that means that
>>> setting up
>>> nrexcl = 3
>>> and
>>> gen-pairs = no
>>> isn't enough
>> In what sense? I suggested in that thread that you look at the contents of
>> the .log files to see if any Coulomb 1-4 interactions exist, but you've not
>> replied. Bald assertions that something doesn't work are likely to get
>> people who might help to assume that the most likely explanation is that
>> you're doing something wrong.
>> Mark
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