[gmx-users] Re: GROMACS and Amber FF

[Anton Feenstra]

Michel Cuendet wrote:

> 
>> for my PhD thesis I am working on DNA with GROMACS. You see the problem?
>>
>>> It seems to be better to use Amber FF for DNA simulations. As I read 
>>> in the mailing list (1 year ago or so), you are/were working on an 
>>> AMBER FF implementation into GROMACS. How far are you? Could I obtain 
>>> it from you?
>>>
>>  
>>
>> Other people have been working on this. Anton Feenstra made a converter
>> from AMBER to GROMACS which requires you to have an AMBER topology. Erik
>> Lindahl and other people in Stanford have worked on a native
>> implementation. I don't know what the status of that is.
>>  
>>
> Hi,
> 
> Yes gromacs works with the AMBER ff, BUT you have to correct the BUG
> for tip3p water in version 3.2.1, already described in this list. It's
> an easy fix to files csettle.c and fsettle.f. Otherwise, your water
> will start to flow across your box, and if you stop the water center of
> mass, your protein will be teared apart.
> 
> This should be WRITTEN BIG on the gromacs website in the converter
> download section. By the way, this converter doesn't work for large
> numbers of atoms. We have a better one here, just mail.

I'm actually running some benchmarks with Gromacs/Abmer and Amber/Amber
to see how they compare. (and, boy, isn't amber s-l-o-w-w-w-w....)


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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