Sure - I added the input files to the Redmine issue. Reza
On May 14, 2013, at 9:21 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 2013-05-13 21:57, Reza wrote: >> So I think I figured out what was causing the discrepancy of Charmm27 >> energies between gromacs and NAMD. It appears that it's related to the >> gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 >> gives energies that are different from both 4.5.7 and NAMD. >> >> Here are the results form my tests on POPC membrane: >> >> =============================== >> BOND ANGLE DIH IMP COUL LJ POT >> gromacs-4.5.7/gromacs.log >> 1539.120 3111.902 1250.540 16.284 -1705.306 -1219.345 >> 2993.188 >> >> gromacs-4.6.1/gromacs.log >> 1539.120 3111.902 1250.540 16.284 -5997.992 350.084 >> 269.945 >> >> namd-2.9/namd.out >> 1539.116 3111.920 1250.542 16.284 -1705.307 -1219.343 >> 2993.211 >> =============================== >> >> >> I think this could be due to either 1) the simulation setup should be >> different between 4.5.7 and 4.6.1 when running single point calculations, or >> 2) my 4.6.1 compilation is not correct (although all regression tests >> passed), or 3) there is a bug somewhere. >> >> I'll attach a script that automates the comparison between GROMACS and NAMD >> in a separate post (it will make this post > 50kB). If you run it and got >> similar/different results as mine, I'll be happy to know. Also any comment >> on the simulations setup is highly appreciated. >> >> Reza > > > Thanks for reporting. I have now created a redmine issue for this > http://redmine.gromacs.org/issues/1249 > Could you please upload the datafiles needed to reproduce this there? > Since gmx 4.5.7 is correct we can use that as a reference. > >> >> >> >> On May 3, 2013, at 11:57 AM, Reza <resa...@gmail.com> wrote: >> >>> >>> Actually pdb which is similarly doesn't have velocity information. In this >>> case however I'm mainly interested to see how the potential terms compare >>> between the two packages with Charmm27 ff. >>> >>> Reza >>> >>> >>>> >>>> >>>> On 5/3/13 11:33 AM, Reza wrote: >>>>> Thanks Mark! >>>>> >>>>>> No, they weren't. See >>>>>> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy >>>>>> You cannot hope to reproduce accurately the energy of a configuration if >>>>>> you let the coordinates be manipulated. >>>>>> >>>>> >>>>> >>>>> The "rerun" option is interesting - in my case however the potential >>>>> energy terms stayed identical but the kinetic term became zero. >>>>> >>>> >>>> If you are using an .xtc file for the rerun, this makes sense since the >>>> .xtc does not store velocities and hence kinetic energy cannot be >>>> calculated. >>>> >>>> -Justin >>>> >>>>>> >>>>>> Something you think is equivalent is not :-) Move to testing a system >>>>>> with >>>>>> two lipids. Inspect all the logfile outputs very carefully for clues. >>>>> >>>>> >>>>> I totally agree :) So far I found out that for "no cut-off" simulation in >>>>> Gromacs, rather that specifying a large cut-off, it needs >>>>> rlist=rvdw=rcoulomb=0 and pbc=no along with ns_type=simple and nstlist=0 >>>>> (according to the manual). I am running various tests and will update if >>>>> I find out what is causing the discrepancy. >>>>> >>>>> Reza >>>>> >>>>> On May 1, 2013, at 5:46 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: >>>>> >>>>>> On Wed, May 1, 2013 at 2:32 PM, Reza Salari <resa...@gmail.com> wrote: >>>>>> >>>>>>> Hi Justin, >>>>>>> >>>>>>> I actually did :) but it ended up being bigger than 50 kb so it needed >>>>>>> moderator approval to show up. I was hoping it would've been released by >>>>>>> now. I'll attach a the details below. >>>>>>> >>>>>>> Any help/hint is highly appreciated. >>>>>>> >>>>>>> Reza >>>>>>> >>>>>>> Details: >>>>>>> >>>>>>> *1)* Both systems were prepared using VMD "membrane" package and then >>>>>>> waters were removed. I used Gromacs 4.6.1 and NAMD 2.9. >>>>>>> >>>>>>> *2)* Simulations were run in vacuum as a single-point energy >>>>>>> calculations >>>>>>> (0 step). >>>>>> >>>>>> >>>>>> No, they weren't. See >>>>>> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy >>>>>> You cannot hope to reproduce accurately the energy of a configuration if >>>>>> you let the coordinates be manipulated. >>>>>> >>>>>> PME was not used. >>>>>>> >>>>>>> *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the >>>>>>> output was saved as the pdb format. The mdp file: >>>>>>> >>>>>>> integrator = md >>>>>>> nsteps = 0 >>>>>>> nstlog = 1 >>>>>>> nstlist = 1 >>>>>>> ns_type = grid >>>>>>> rlist = 100.0 >>>>>>> coulombtype = cut-off >>>>>>> rcoulomb = 100.0 >>>>>>> rvdw = 100.0 >>>>>>> pbc = no >>>>>>> >>>>>>> *4) *NAMD input file: >>>>>>> >>>>>>> structure ../0_prep/memb_nowat.psf >>>>>>> paratypecharmm on >>>>>>> parameters par_all27_prot_lipid.prm >>>>>>> exclude scaled1-4 >>>>>>> 1-4scaling 1.0 >>>>>>> switching off >>>>>>> switchdist 8 >>>>>>> cutoff 1000 >>>>>>> pairlistdist 1000 >>>>>>> margin 0 >>>>>>> timestep 1.0 >>>>>>> outputenergies 1 >>>>>>> outputtiming 1 >>>>>>> binaryoutput no >>>>>>> coordinates ../0_prep/memb_nowat.pdb >>>>>>> outputname out >>>>>>> dcdfreq 10 >>>>>>> temperature 300 >>>>>>> run 0 >>>>>>> >>>>>>> *5)* Energies: >>>>>>> >>>>>>> For Single POPC (kcal/mol) >>>>>>> >>>>>>> >>>>>>> Gromacs NAMD Diff >>>>>>> >>>>>>> Bond 43.0022 43.0015 -0.0007 >>>>>>> Angle 80.6568 80.6571 0.0003 >>>>>>> Dih 29.8083 29.8083 0.0000 >>>>>>> Imp 0.8452 0.8452 0.0000 >>>>>>> >>>>>>> Coul -17.2983 -17.2983 0.0000 >>>>>>> LJ -7.0798 -7.0798 0.0000 >>>>>>> >>>>>>> Pot 129.9343 129.9340 -0.0003 >>>>>>> >>>>>>> >>>>>> The intra-molecule terms look fine. Since this is a lipid, there are >>>>>> non-bonded interactions that are intra-molecule, so the non-bondeds also >>>>>> seem fine. >>>>>> >>>>>> For POPC Memb (kcal/mol) >>>>>>> >>>>>>> Gromacs NAMD Diff >>>>>>> >>>>>>> Bond 1539.1181 1539.1162 -0.0019 >>>>>>> Angle 3111.9264 3111.9197 -0.0067 >>>>>>> Dih 1250.5425 1250.5421 -0.0004 >>>>>>> Imp 16.2837 16.2837 0.0000 >>>>>>> >>>>>>> Coul -1837.8585 -1705.3075 132.5510 >>>>>>> LJ -995.0311 -1219.3432 -224.3121 >>>>>>> >>>>>>> Pot 3084.9904 2993.2110 -91.7794 >>>>>>> >>>>>> >>>>>> Something you think is equivalent is not :-) Move to testing a system >>>>>> with >>>>>> two lipids. Inspect all the logfile outputs very carefully for clues. >>>>>> >>>>>> Mark >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 4/30/13 4:19 PM, Reza Salari wrote: >>>>>>>> >>>>>>>>> Hi >>>>>>>>> >>>>>>>>> I have set up two small systems, one with a single POPC lipid, and >>>>>>> another >>>>>>>>> system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a >>>>>>>>> similar comparison as in Table 1 in the Par Bjelkmar et al paper >>>>>>> (porting >>>>>>>>> charmm ff to gromacs) for my systems. My main question is that for the >>>>>>>>> single POPC, all the potential energy terms match very well, but for >>>>>>>>> the >>>>>>>>> membrane system the non-bonding terms differ significantly. >>>>>>>>> >>>>>>>>> I am providing the full details below and greatly appreciate any hint >>>>>>> for >>>>>>>>> better comparison of the energies. >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Reza Salari >>>>>>>>> >>>>>>>>> Details: >>>>>>>>> >>>>>>>>> 1) Both systems were prepared using VMD "membrane" package: >>>>>>>>> >>>>>>>>> 2) >>>>>>>>> >>>>>>>>> >>>>>>>> It appears you hit "send" too early. Please provide the entirety of >>>>>>>> the >>>>>>>> details you intended. Complete .mdp files and actual quantification of >>>>>>> the >>>>>>>> differences you are observing are also very important. >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>> -- >>>>>>>> ==============================**========== >>>>>>>> >>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>> Research Scientist >>>>>>>> Department of Biochemistry >>>>>>>> Virginia Tech >>>>>>>> Blacksburg, VA >>>>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>>>>>> >>>>>>>> ==============================**========== >>>>>>>> -- >>>>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>>>> * Please search the archive at http://www.gromacs.org/** >>>>>>>> Support/Mailing_Lists/Search< >>>>>>> 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< >>>>>>> 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 >>>>> >>>> >>>> -- >>>> ======================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Research Scientist >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> -- >>>> 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 >>> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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
