On Tue, Jan 24, 2017 at 10:48 AM, Rodriguez, Yoel
<yoel.rodriguez.mssm.edu> wrote:
> 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:
If you are going to RMS-fit, then yes it needs to be after imaging
(otherwise you can't image). However once you RMS-fit you are
destroying the periodicity of your system because the coordinates no
longer align with the unit cell vectors. So in the end what you're
observing is a visual artifact from the RMS-fit of your system.
> # first center the solute by itself (lipids)
> center origin :997-2199
> #
> # now image the whole system about the centered origin
> autoimage
Note that this sequence of commands isn't doing what you think. The
'autoimage' command centers and images according to an "anchor"
molecule, so any previous center/image commands essentially don't
matter. If you really want something centered on the origin add the
'origin' keyword to 'autoimage'.
-Dan
> #
> #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
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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://www.lobos.nih.gov/lcb
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Received on Tue Jan 24 2017 - 11:00:03 PST
