[gmx-users] How to use ambconv package...

[david.evans at ulsop.ac.uk]

All I did was to compare the single point energies, from the start of
a minimisation. I used the AMBER DNA tutorial on the website as a
test system (bearing in mind that Gromacs uses kJ/mol and nm :)).

I don't know how significant the differences are, my guess would be
that ~1% might be due to differences in coding and the fact that
gromacs is single-precision and AMBER double precision. (Which
reminds me I should test the double-precision version of gromacs).
The 10% I was more concerned about. It may well be that relative
energies are not significantly affected, but I have not yet had time
to compare results of long simulations with Gromacs/AMBER.
If any Gromacs gurus have an opinion, that would be helpful.

Dave

---- Message from Tomas Kubar <tomas.kubar at uochb.cas.cz> at
2004-06-18 13:05:58 ------
>Hi Dave
>
>david.evans at ulsop.ac.uk wrote:
>> Hi, Tomas,
>> 
>> Are you using ambconv regularly?
>
>Yes. Predominantly for isolated bases and DNA duplexes.
>
>> I managed to get it working, but was
>> slightly concerned that the energies between AMBER and Gromacs did
>> not agree so well (~1% difference for isolated DNA duplex, ~10% for
>> VdW in a solvated DNA duplex), compared to Filip Ryjacek's stated
>> accuracy of 0.01%. I was wondering if you had managed to get better
>> accuracy.
>
>I did not test it as properly as you did, I guess. Could you desribe 
>your tests in more detail to make me able to reproduce them? I
suppose 
>you are talking about interaction energy..
>
>Thank you
>tomas
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