[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

[Mark Abraham]

On Wed, May 1, 2013 at 2:32 PM, Reza Salari <resal81 at 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 <jalemkul at 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 at 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-request at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>