On 9/20/16 1:17 PM, 凌未风 wrote:

I am simulating a stearol sphingomyelin bilayer with 81 lipids in each
leaflet using the CHARMM force field. I used the CHARMM-GUI to generate the
initial conformation, as well as the parameters for mdp file. I conducted the
simulation by gmx5.0.4.

I found a significant smaller area per lipid (APL) in my simulations. The APL
kept on decreasing, and started to equilibriated after 400 ns. The expected
value is ~55.4 A^2, but in my simulation, the value was ~50.8 A^2 after
equilibrated. For me this difference is significant. I looked up in the
mailing list, and found someone said that it is because of the ions using or
it is because of the motion of the two leaflets. So I tried simulations
without ions, and with NaCl/KCl. I also tried to remove the centers of mass
of two leaflets separately in my simulations. But all of the simulations
generated similar APL.

I am really appreciate for any possible suggestions. This looks really
strange for me, as I am using the "standard parameters" (i.e., the parameters
generated by CHARMM-GUI) for CHARMM force filed in gromacs, and the
difference should not be so larger, if there are any differences....

The values should be in better agreement; we validated PSM as part of the latest CHARMM-GUI update. You're using the .mdp files directly from CHARMM-GUI, right? What temperature have you set?


Thanks again for any help you may provide.

Cheers, RXG University of Calgary


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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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