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

[Broadbent, Richard]

Dear Marcelo,

I think you need to calm down. You are using a very nice piece of free code which has in excellent documentation as well as being open source.

If you are using a piece of software in a non-standard way it stands to reason that it might not be documented.  When this occurs in my research I simply run some test cases so that I can understand what is going on, or I refer to the source code which is available for all to see. These two approaches allow you to understand everything about how Gromacs functions. 

I do not know what your problem in the context of pair potential interactions in Gromacs is as you have failed to give any details, and therefore did not respond. Those who did respond directed you to sources of information which you ignored. 

The users of this mailing list and the Gromacs developers give up their time to assist others, insulting any of them is very offensive. 

Yours Sincerely,

Richard Broadbent







-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Marcelo Lopez
Sent: 07 May 2012 10:39
To: Discussion list for GROMACS users
Subject: Fwd: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

You didn't reply the part where I told "unless you're trying to have some advantage"...


---------- Forwarded message ----------
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Date: 2012/5/6
Subject: Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


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 understandable.

Mark


> 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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