Hello Daniel,
Thanks very much for your reply.
I posted in my previous message the imagine protocol I have been using. I do RMS-fitting, but after doing imaging. Isn't it correct? Here is a summary of the whole script using cpptraj:
cpptraj
trajin ../../EQ/1.rst.gz
trajin ../../EQ/2.rst.gz
...
trajin ../../EQ/200.rst.gz
# first center the solute by itself (lipids)
center origin :997-2199
#
# now image the whole system about the centered origin
autoimage
#
#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"
#
rms first out protein_CA.dat ":1-994.CA"
#
#rms the protein
rms first out ligand.dat ":995" nofit
#
#write the trajectory
trajout protein_memb.trj
Thanks once again!
Best,
Yoel
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, January 24, 2017 8:23 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Pure POPC Membrane Tilts during MD simulation
Can you post the script you are using for post-processing? This looks
to me like you are performing RMS-fitting, which will destroy any
periodicity in your system since it rotates the coordinates out of
alignment with the unit cell.
-Dan
On Sat, Jan 21, 2017 at 7:21 PM, Rodriguez, Yoel
<yoel.rodriguez.mssm.edu> wrote:
> 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 (md.in) 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!
>
> Best,
> Yoel Rodriguez, PhD
> The City University of New York
> Mount Sinai School of Medicine
>
> md.in file
>
> 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
>
> ! 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)
>
> ! 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=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
> iwrap=1,
>
> ! 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
> /
>
> /
> &ewald
> skinnb=5, ! Increase skinnb to avoid skinnb errors
> /
>
>
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>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.lobos.nih.gov_lcb&d=DQICAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=hVgs2MTRFepPtJy5rTN5kTyTBgyQpf_ydrz5RjxxmQs&m=dDEER9VmUjtJeKjgn6_JgQJ-McpBZygQiQyW2Sgb_B4&s=qVBmDZyjUMC4Bxsw7wTrYaLkEDZckZrRkhp1lYiej_4&e=
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Received on Tue Jan 24 2017 - 08:00:04 PST
