[gmx-developers] Re: Source code

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 15 00:06:49 CEST 2009

??????? ????? wrote:
> Dear Mr. Abraham
> My apologies if this email disturb you. I am a Ph.D. student in USA. I 
> am doing the development of algorithm fo MD simulation by utilizing 
> gromacs. I have to implement the algorithm in the gromacs code.

As a general principle, please leave GROMACS correspondence on the 
mailing lists unless you already know it's only of personal interest to 
the recipient. That means it pertains directly to their published work, 
or they know you :-) This practice means the discussion gets archived 
and multiple people can contribute to and learn from the discussion, if any.

> So far I have learnt how to do the basic NVE NVT NPT simulation and 
> known the process how to simulate in the gromacs program.
> Thus, my problem is that I have no idea with gmx source code where can I 
> find it or how to change the code and execute it.
> Could you give me suggestions please?

You find the source code on the website. You have a large learning curve 
in front of you to understand it before modifying it might be 
reasonable. You need to understand that the bulk of the code establishes 
a framework in which the nonbonded loops execute many times quickly and 
efficiently. As was pointed out to you earlier on the mailing list, 
there is a lot of relevant material on the wiki which will be of some 
help. There is no substitute for breaking out a debugger and following 
the flow of the program, however. When you come to making your strategy 
choices, advice on your approach from an experienced GROMACS developer 
could be extremely valuable.

> Thank you very much for advance. Looking forward hearing from you.


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