Just to add to that -
The non-polar term of GBSA do not match between gmx and Amber11, presumably
due to different algorithms for computing the surface area.
I tried the different surface area options (gbsa keyword) in Amber11, but
it didn't help.
fyi.
Best
Sandeep
On Fri, Nov 9, 2012 at 8:32 A
After some investigation, it turns out that this is explained by the
differences in input radii for the GB-calculation done by Gromacs and Amber.
The radii in the gbsa.itp-file are not the same as the ones used by Amber.
If one changes the radii in gbsa.itp, you get a difference in 0-step energy
Hi Per
I tried with single precision gmx as well. No change.
Will send you input files soon.
Best
Sandeep
On Thu, Nov 8, 2012 at 3:55 PM, Per Larsson wrote:
> Hi
>
> Thanks for doing those test. They are all reassuring, I think.
> Could you maybe send me your input-files off list and I'll tak
Hi
Thanks for doing those test. They are all reassuring, I think.
Could you maybe send me your input-files off list and I'll take a look.
I suspect the issue is that different radii are being used, as Gromacs does not
use the Bondi radii.
Cheers
/Per
8 nov 2012 kl. 16:35 skrev Sandeep Somani:
Hi Per
Pls see inline comments:
> 1. If I recall correctly, the GB-energy in gromacs is split into two
> parts, GB-polarization and non-polar solvation. Can you check whether this
> is the case and if the value you report is the sum of those two terms.
>
Yes, gromacs prints out "GB Polarization
Hi
A few things:
1. If I recall correctly, the GB-energy in gromacs is split into two parts,
GB-polarization and non-polar solvation. Can you check whether this is the case
and if the value you report is the sum of those two terms.
2. Try setting all cut-offs to 0 (infinite cutoffs). That will
Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to re
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