[gmx-users] Re: Starting configuration for gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 28 23:03:09 CET 2008

Luis Javier Alvarez wrote:
> Dear Mark:
> Thanks for your response to my mail on the initial configuration for 
> gromacs. Since in your reply you implicitly posed some questions I am 
> writing directly to you to ask you something in the hope that it shall 
> not bother you.

Please leave gromacs-related correspondence on the list. That way it's 
archived for others to find later.

> You mentioned that there is the question of wether or not we have access 
> to the right tools to set up the initial configuration for gromacs to 
> generate the topology file. In fact we do not have anything specialised. 
> We are using what we can get from the internet and if necessary we write 
> our own programs. So the question is: what are these right tools?

Various force fields have tools that are suited for topology-generation, 
like Antechamber or PRODRG or x2top or pdb2gmx, and your choice of force 
field will be connected with the availability of such tools and the 
nature of your simulation system.


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