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 <per.lars...@sbc.su.se> 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 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 > -- 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