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
