[gmx-users] Reproducing Charmm36 POPC electron density

[Gmx QA]

Hi Justin,

Thanks, that's reassuring then. My reason for worrying was in part because
the reported electron densities in several papers I have read seem to match
very closely. But since as you say the APL values also agree then
everything might be ok after all?

Thanks
/PK


2016-02-24 15:52 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 2/24/16 7:25 AM, Gmx QA wrote:
>
>> Dear list
>>
>> I have a simulation of a system of 64 POPC lipids per leaflet using the
>> Charmm36 lipid parameter set, and I am calculating the electron density
>> across the bilayer to compare to literature values. Unfortunately I cannot
>> quite get the same results as eg. in Klauda et al (
>> http://www.sciencedirect.com/science/article/pii/S0005273614002193)
>>
>> I have made the starting structure using the charmm-gui, and gone through
>> all the equilibration steps as suggested in the gromacs tar-ball from that
>> website.
>>
>> My production mdp file is the following:
>>
>> integrator              = md
>> dt                      = 0.002
>> nsteps                  = 50000000
>> nstlog                  = 10000
>> nstxout                 = 500000
>> nstvout                 = 500000
>> nstfout                 = 0
>> nstcalcenergy           = 10
>> nstenergy               = 1000
>> nstxtcout               = 500000
>> ;
>> cutoff-scheme           = Verlet
>> nstlist                 = 20
>> rlist                   = 1.2
>> coulombtype             = pme
>> rcoulomb                = 1.2
>> vdwtype                 = Cut-off
>> vdw-modifier            = Force-switch
>> rvdw_switch             = 1.0
>> rvdw                    = 1.2
>> ;
>> tcoupl                  = Nose-Hoover
>> tc_grps                 = POPC SOL
>> tau_t                   = 1.0 1.0
>> ref_t                   = 303.15  303.15
>> ;nsttcouple = 1
>> ;
>> pcoupl                  = Parrinello-Rahman
>> pcoupltype              = semiisotropic
>> tau_p                   = 5.0 5.0
>> compressibility         = 4.5e-5 4.5e-5
>> ref_p                   = 1.0 1.0
>> ;
>> constraints             = h-bonds
>> constraint_algorithm    = LINCS
>> continuation            = yes
>> ;
>> nstcomm                 = 10
>> comm_mode               = linear
>> comm_grps               = POPC SOL
>> ;
>> refcoord_scaling        = com
>>
>> Simulations are run with gromacs 5.0.4, and currently 100 ns long.
>>
>> Before running vmx density, I center my trajectory like this:
>> $ gmx trjconv -f run.trr -s em.tpr -o run_center.trr -center
>>
>> selecting POPC as the group to center on.
>>
>>   Then, my command for computing the electron density is the following
>> (also
>> using gmx density 5.0.4):
>>
>> $ gmx density -f run_center.trr -s em.tpr -o  density_traj_center.xvg
>> -dens
>> electron -ei electrons.dat -center
>>
>> Again, selecting POPC to center the density profile on.
>>
>> The resulting profile can be found here (i hope that works)
>> http://www.filedropper.com/compareelectrondensity
>>
>> As you can see, the depth of the central trough is not as deep as the
>> literature value, nor is the height of the density the same even though
>> the
>> peak-peak distance appears to be similar, and values in the other regions
>> also match _fairly_ closely.
>>
>> The average APL value over the entire trajectory is 64.0 +- 1.33, which is
>> in line with the reported 64.7 from Klauda, but the electron density
>> worries me a bit. Perhaps anyone (Justin?) can shed any light on this?
>>
>>
> Why?  The results match almost perfectly.  The magnitude of error is
> within a few % and if your APL matches then I'm sure everything is fine.
> We rigorously tested the lipid inputs, cutoff setup, etc. and everything
> agrees quite well between lipid simulations in CHARMM, GROMACS, AMBER,
> NAMD, and OpenMM.  There are minor variations, as would be expected in
> comparing any two software programs, but nothing is really aberrant.
>
> http://dx.doi.org/10.1021/acs.jctc.5b00935
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>