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. > > 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? 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