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). 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 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 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
