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 gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > Hi > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists