Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

2011-11-24 Thread Thomas Evangelidis
Hi Oliver, Apologies for the late reply. The comparison you have showed us has been done for a DNA fragment. Do you believe that negligible errors can also be obtained for proteins using the amber99sb force field? thanks, Thomas On 22 November 2011 11:58, Oliver Grant wrote: > Hi there, > >

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

2011-11-22 Thread Oliver Grant
Hi there, Acpype does the conversion for you and the results from their own testing are here: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx For reproducing experimental data I would look in the original force-field publications. Oliver On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

2011-11-21 Thread Michael Shirts
> Is anyone aware of any benchmark analysis about the implementation of the > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in > GROMACS and AMBER. I am interested to know in what extend the energies > correlate and if the results agree with experimental data. Whether the res

[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

2011-11-21 Thread Thomas Evangelidis
Dear GROMACS users, Is anyone aware of any benchmark analysis about the implementation of the amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in GROMACS and AMBER. I am interested to know in what extend the energies correlate and if the results agree with experimental data. Di