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 (at least for the system below) of 0.2 kJ/mol, which is tolerable. I have pasted a copy of the gbsa.itp-file below, in case it is useful for someone. This was tested with amber99sb. Cheers /Per [ implicit_genborn_params ] ; atype sar st pi gbr hct ;Br 0.1 1 1 0.125 0.85 ; H C 0.172 1 1.554 0.17 0.72 ; C CA 0.18 1 1.037 0.17 0.72 ; C CB 0.172 0.012 1.554 0.17 0.72 ; C CC 0.172 1 1.554 0.17 0.72 ; C CN 0.172 0.012 1.554 0.17 0.72 ; C CR 0.18 1 1.073 0.17 0.72 ; C CT 0.18 1 1.276 0.17 0.72 ; C CV 0.18 1 1.073 0.17 0.72 ; C CW 0.18 1 1.073 0.17 0.72 ; C C* 0.172 0.012 1.554 0.17 0.72 ; C H 0.1 1 1 0.13 0.85 ; H HC 0.1 1 1 0.12 0.85 ; H H1 0.1 1 1 0.12 0.85 ; H HA 0.1 1 1 0.12 0.85 ; H H4 0.1 1 1 0.12 0.85 ; H H5 0.1 1 1 0.12 0.85 ; H HO 0.1 1 1 0.12 0.85 ; H HS 0.1 1 1 0.12 0.85 ; H HP 0.1 1 1 0.12 0.85 ; H N 0.155 1 1.028 0.155 0.79 ; N NA 0.155 1 1.028 0.155 0.79 ; N NB 0.155 1 1.215 0.155 0.79 ; N N2 0.16 1 1.215 0.155 0.79 ; N N3 0.16 1 1.215 0.155 0.79 ; N O 0.15 1 0.926 0.15 0.85 ; O OH 0.152 1 1.080 0.15 0.85 ; O O2 0.17 1 0.922 0.15 0.85 ; O S 0.18 1 1.121 0.18 0.96 ; S SH 0.18 1 1.121 0.18 0.96 ; S ; masscenters for vsites do not have gbsa parameters MNH3 0 0 0 0 0 MCH3 0 0 0 0 0 8 nov 2012 kl. 23:42 skrev 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 <[email protected]> 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 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" and "Nonpolar Sol." >>> corresponding to "EGB" and "ESURF", respectively, from Amber. >>> Right now I am just comparing EGB part (non polar also do not match but >>> since it is a much smaller contribution, will worry about that later!). >>> >>> >>> >>>> >>>> 2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a >>>> slightly different part of the code to do the GB-calculation (you should >>>> see in your log file references to all-vs-all kernels) >>>> >>> >>> Just tried -- no change. >>> (btw, i didnt know 0 => no-cutoff. thnx!) >>> >>> >>>> >>>> 3. Try running in single precision, keeping in mind 1 and 2 above to see >>>> if that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to >> 1 >>>> (at least it used to be called that, someone else can perhaps correct >> me if >>>> that has changed). This will make the code run without the sse-loops. >>>> >>>> I'll try shortly. >>> >>> >>>> 4. It could be that you are using different radii for the atoms in your >>>> system. For amber, are you using the Bondi-radii or something else? >>>> >>>> I tried both "set default PBradii mbondi" and "set default PBradii >>> mbondi2" while creating amber prmtop files in leap. The difference in EGB >>> is just 2-3 kcal/mol .. not enough to bridge the gap. >>> >>> Best >>> Sandeep >>> >>> >>> >>> >>> >>> >>> >>>> Cheers >>>> /Per >>>> >>>> >>>> 8 nov 2012 kl. 05:43 skrev 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 replicate Amber's "igb=5 + large cutoff" in >> gmx. >>>>> According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC >>>>> paper]". >>>>> >>>>> I translated this to the following mdp options: >>>>> ---- >>>>> implicit_solvent = GBSA >>>>> gb_algorithm = OBC >>>>> All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of >>>> the >>>>> molecule. >>>>> {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, >>>> gb_obc_gamma, >>>>> gb_dielectric_offset} = corresponding Amber input. >>>>> ---- >>>>> >>>>> Is that correct? >>>>> >>>>> I realize that this is as much a question for Amber mailing list, but >>>>> trying here first! Any idea? >>>>> >>>>> The molecule is ala-12. I'll be happy to send input files. >>>>> >>>>> Thanks in advance >>>>> >>>>> Sandeep >>>>> >>>>> -- >>>>> Postdoc >>>>> Wales Group >>>>> Cambridge >>>>> -- >>>>> gmx-users mailing list [email protected] >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to [email protected]. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> * Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected]. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> Hi >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
