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

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Fri Jun 18 14:02:19 CEST 2004

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.


---- 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
>you are talking about interaction energy..
>Thank you
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: david_evans.vcf
Type: text/directory
Size: 160 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040618/e82183f9/attachment.bin>

More information about the gromacs.org_gmx-users mailing list