Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-09 Thread Sandeep Somani
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

Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-09 Thread Per Larsson
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

Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-08 Thread Sandeep Somani
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

Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-08 Thread Per Larsson
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:

Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-08 Thread 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

Re: [gmx-users] comparing gmx GB energy with Amber11

2012-11-08 Thread Per Larsson
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

[gmx-users] comparing gmx GB energy with Amber11

2012-11-07 Thread Sandeep Somani
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