On 9/20/16 4:03 PM, 凌未风 wrote:
Hi Justin,


I am using a temperature of 323 K, but I am using SSM instead of PSM. Does this 
make difference?


No, but there is no reason why PSM should work and SSM wouldn't.

PS: not sure this is the best way to reply in a mailing list

It works like any other email. Just reply to gmx-us...@gromacs.org (which should be the default reply-to address) and the mailing list sends it out to everyone.

-Justin







On 9/20/16 1:17 PM, ??? wrote:
Hello:


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?

-Justin


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
http://mackerell.umaryland.edu/~jalemkul

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