Re: [AMBER] Problems with MC barostat

From: Gomez, Yessica <Yessica.Gomez.ucsf.edu>
Date: Sat, 1 Aug 2020 00:51:23 +0000

Hello again,

I am replying to myself for two reasons:


  1. Boost visibility as I'm still really hoping that someone can help me with these membrane protein simulations!
  2. I would like to add an external reference to my original statement: Wonpil Im and Martin Zacharias have recently published a report in which they also seem to observe severe membrane defects when using the MC barostat + amber ff + semi-isotropic pressure coupling. https://doi.org/10.1063/5.0012280.jcp.2020.CLMD2020.issue-1 (see Fig. S1)

Hoping this works,


Yessica Gomez

________________________________
From: Yessica <yessica.gomez.ucsf.edu>
Sent: 12 July 2020 16:53
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Problems with MC barostat

Dear AMBER folks,

I have been doing fully atomistic simulations of a protein in a POPC
bilayer using AMBER18 with the AMBER forcefields. The system has
~305,000 atoms and box dimensions of 200x200x80.
I have repeatedly encountered a problem where after ~100ns of
unrestrained (production) simulation it becomes apparent that the box is
shrinking in the X and Y dimensions, while growing in the Z dimension.
This behavior is seen for multiple systems of the same size. For
production, I use the following parameters:

A NPT simulation for common production-level simulations
  &cntrl
     imin=0, ! No minimization
     irest=1, ! This IS a restart of an old MD simulation
     ntx=5, ! So our inpcrd file has velocities
     ig=-1,

     ! Temperature control
     ntt=3, ! Langevin dynamics
     gamma_ln=1.0, ! Friction coefficient (ps^-1)
     temp0=303.15, ! Target temperature

     ! Potential energy control
     cut=10.0, ! Nonbonded cutoff, in Angstroms

     ! MD settings
     nstlim=100000000, ! 100M steps, 200 ns total
     dt=0.002, ! time step (ps)

     ! SHAKE
     ntc=2, ! Constrain bonds containing hydrogen
     ntf=2, ! Do not calculate forces of bonds containing hydrogen
     tol=0.0000001, ! SHAKE tolerance

     ! Control how often information is printed
     ntpr=100000, ! Print energies every 100K steps
     ntwx=100000, ! Print coordinates every 100K steps to the trajectory
     ntwr=100000, ! Print a restart file every 100K steps (can be less frequent)
     ntxo=2, ! Write NetCDF format
     ioutfm=1, ! Write NetCDF format (always do this!)

     ! Wrap coordinates when printing them to the same unit cell
     !iwrap=1,

     ! Constant pressure control.
     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
     taup=1.0, ! Was 10 in Yessica's mineq but has been reset to default here

     ! 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)
     ntb=2, ! pbc
  /
   &wt type='END' / ! End of varying conditions
  /
LISTIN=POUT
LISTOUT=POUT
&end
END

However, if I start a parallel simulation with the same parameter files
using the Berendsen barostat instead of MC (only change is barostat=1),
I do NOT observe the box compression even at 200+ ns of run-time. I
believe this also speaks to the question raised by David Case in a
recent thread: https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_202006_0010.html&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=T6US3N2WegwU9JTvFqVV6BrQCcV4GRxsMY2PlJIZeTQ&m=5yesiHzNuv2S08M6LQ0nIVToRHgNt2X9W5Cs7r1wAyE&s=C2gauOgGzWZMkcxd_vENN6s-JoXXBo7vKrGicBaEvWQ&e=

Why might this be happening, and is there a way I can fix it?

--
Yessica
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Received on Fri Jul 31 2020 - 18:00:02 PDT
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