Re: [AMBER] Pure POPC Membrane Tilts during MD simulation

From: Rodriguez, Yoel <>
Date: Tue, 24 Jan 2017 15:41:26 +0000


Thanks very much!

I have used cpptraj and ptraj and I got the same results. Here are the imaging protocols I have used:


trajin ../../EQ/1.rst.gz
# first center the solute by itself (lipids)
center origin :997-2199
# now image the whole system about the centered origin


#rms the protein
rms first out rms_memb.dat ":48-56,59-76,88-112,247-275,287-307,310-328,739-781,788-798,800-808,831-857,893-914,951-957,963-991"


trajin ../../EQ/1.rst.gz
# first center the solute by itself (lipids)
center origin :997-2199
# now image the whole system about the centered origin (ligand)
image origin center familiar com :995
#rms the protein
rms first out rms_memb.dat ":48-56,59-76,88-112,247-275,287-307,310-328,739-781,788-798,800-808,831-857,893-914,951-957,963-991"


From: Dickson, Callum J []
Sent: Monday, January 23, 2017 5:41 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Pure POPC Membrane Tilts during MD simulation


Have you tried a few different imaging protocols with cpptraj?

Maybe it is the protein that tilts during the simulation; the imaging with cpptraj anchors the protein making it seem that it is the bilayer tilts rather than the protein?



From: Rodriguez, Yoel <>
Sent: Saturday, January 21, 2017 7:21:52 PM
To: AMBER Mailing List
Subject: [AMBER] Pure POPC Membrane Tilts during MD simulation

Dear Amber Community:

I have used CHARMM-GUI to build my membrane made of pure POPC lipids. Then I followed AMBER Tutorial 16 and the README file generated in the amber folder of CHARMM-GUI to prepare all my files for minimization, equilibration and production.

The MD production seemed to have run without any problem, but during its analysis I have been finding that the membrane tilts back and forth during the MD simulation. I used the autoimage option in cpptraj to image the whole system about a centered origin.

Please, find attached the input file ( I used to run the NPT production and a pdf file with different snapshots of the centered system along the MD simulation (200 ns). Periodic images are drawn on the +X, -X, +Z and -Z directions using VMD.

The membrane is on the XY plane and the protein is along the Z axis.

Could you please give me some input on this behavior?

Thanks very much for you help!

Yoel Rodriguez, PhD
The City University of New York
Mount Sinai School of Medicine file

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

! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
temp0=310, ! Target temperature
ig=-1, ! The random seed will be based on the current date and time, and hence will be different for every run

! Potential energy control
cut=8.0, ! nonbonded cutoff, in Angstroms
ntb=2, ! periodic boundary conditions for calculation of non-bonded interactions

! MD settings
nstlim=500000, ! 500K steps, 1 ns total
dt=0.002, ! time step (ps)

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=2500, ! Print energies every 2500 steps
ntwx=2500, ! Print coordinates every 2500 steps to the trajectory
ntwr=2500, ! Print a restart file every 2500 steps (can be less frequent)
ntwe=2500, ! Pring energies and temperatures every 2500 to file "mden"
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=1, ! Write Formatted (ASCII)
ioutfm=0, ! Formatted ASCII trajectory

! Wrap coordinates when printing them to the same unit cell

! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=2, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)

! 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)

! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O

skinnb=5, ! Increase skinnb to avoid skinnb errors

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Received on Tue Jan 24 2017 - 08:00:03 PST
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