[gmx-users] NVT or NPT ensemble?

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 3 18:01:22 CET 2005

On Thu, 3 Feb 2005, Hendrik Preuss wrote:

>Hi all,
>I need your help to decide which ensemle to use for my simulation.
>I generated a system consisting of a GPCR in a POPC bilayer (81
>monomers) that is solvated with spc water (in a triclinic box). 10 Cl
>cations were included to have total charge of 0. I work with the ffgmx
>FF and the lipid.itp and popc.itp from the group of Dr. Tieleman.
>First I tried the following settings in my mdp file for 500 ps
>equillibration (protein fixed):
>;electrostatics and vdw
>coulombtype              = PME
>vdwtype                  = Cut-off
>rcoulomb                 = 1.4
>rvdw                     = 1.0
You can make thae the reverse:
rouclomb = 1.0
rvdw     = 1.4
rlist    = 1.0

>DispCorr                 = EnerPres
>optimize_fft             = yes
>;temperature coupling
>tcoupl                   = berendsen
>tc-grps                  = Protein      POP  SOL Cl
>tau_t                    = 0.1  0.1  0.1 0.1
>ref_t                    = 300  300  300 300
>;pressure coupling
>pcoupl                   = berendsen
>tau_p                    = 1.0
>pcoupltype               = isotropic
>compressibility          = 4.5e-5
>ref_p                    = 1.0
Make that anisotropic with tau_p at least 5 ps.

>With these settings the volume of my box decreased from 404 nm^3 to 347
>nm^3 during the first 40 ps (the pressure of the system at the beginning
>was -2495 bar). During 500 ps the thickness of the lipid bilayer is
>diminished such that the transmembrane domains are no longer surrounded
>by lipid but water.
>Therefore I decided to keep the volume constant in a new run (pcoupl =
>But then, the lipids changed to disordered conformations and regions
>with "empty space" appeared. In this case the pressure fluctuates
>between -500 and -1000 bar.
>Do you have an idea what to do? What is the correct ensemble type in my
>Thanks a lot for your help!
>Hendrik Preuss
>Institute of Pharmacy
>University of Regensburg
>D-93040 Regensburg, Germany
>Phone: +49 941 943 3329
>e-mail: hendrik.preuss at chemie.uni-regensburg.de
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list