[AMBER] Barostat options for membrane protein simulations in NPT

From: James Starlight <jmsstarlight.gmail.com>
Date: Wed, 2 Aug 2017 17:21:15 +0200

Dear Amber users!

Recently I have tested charm-gui output provided for the membrane
protein system prepared for AMBER simulations. Here Charmm-gui
prepared systems for Amber-16 with CHARM36 param-sets. My questions is
regarding mdin files provided by charnn-gui, mainly for the barostat

Here they propose to use MC barostat with semi-isotropic coupling with
enabled surftension in xy planes for 2 interlaces.

 barostat=2, ! MC barostat... change to 1 for Berendsen
    ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
    pres0=1.0, ! Target external pressure, in bar

    ! Constant surface tension (needed for semi-isotropic scaling). Uncomment
    ! for this feature. csurften must be nonzero if ntp=3 above
    csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
    gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
    ninterface=2, ! Number of interfaces (2 for bilayer)

Does these params provide more true physical behavior of the bi-layer
system compared to what I have used with Amber99sb ff for the same
systems modeled in NPT ensemble with Berendsen barostat and
anisotropic coupling ?
ntb=2, ! Constant pressure periodic boundary conditions
  ntp=2, ! Anisotropic pressure coupling

I thanks so much for help!


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Received on Wed Aug 02 2017 - 08:30:03 PDT
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