> However, i do still have a bunch of molecules that appear on opposite
> edges of the box in some instances and in other cases, they appear on
> the four corners of the box. They are still resistant to being centered
> in the middle of the box.
Are you running NPT (constant pressure, NTP=1); sounds like vacuum bubble
due to incorrect box size in NVE/NVT simulation. Otherwise, we would need
more information to decipher the issue. --tec3
> >> ntc=2, ntf=2, gamma_ln = 2.0,
> >> ntwx=200, ntwr=100, ioutfm=1,
> >> ntr=1, restraintmask=':1-54', restraint_wt=25.0,
> >> nmropt=1
> >> /
> >> &wt TYPE='TEMP0', istep1=0, istep2=100000,
> >> value1=0, value2=300.0, /
> >> &wt TYPE='END' /
> >>
> >> Equilibration 2:
> >> CZRA : equilibration
> >> &cntrl
> >> nstlim=500000, dt=0.002,ntx=7,irest=1,ntpr=1000,ntwx=1000,
> >> tempi=300.0, temp0=300.0, ntt=3, imin=0, ntwv=-1,
> >> ntb=2, cut=8,ig=-1,ntwr=1000,
> >> pres0 = 1.0, ntp = 1, iwrap=1,
> >> taup = 2.0, ig=-1,
> >> ntc=2, ntf=2, gamma_ln = 2.0,
> >> ioutfm=1,
> >> /
> >> &ewald
> >> /
> >> ~
> >> Minimisation 1:
> >> minimize structure
> >> &cntrl
> >> imin=1,maxcyc=20000, ncyc=5000,
> >> ntb=1, cut=8, ntwx=500, ioutfm=1,iwrap=1,
> >> ntr=1, restraintmask=':1-54', restraint_wt=200.0,
> >> /
> >> &ewald
> >> /
> >>
> >> Minimisation2:
> >> minimize structure
> >> &cntrl
> >> imin=1,maxcyc=20000, ncyc=5000,
> >> ntb=1, cut=8, ntwx=500, ioutfm=1,iwrap=1,
> >> ntr=1, restraintmask=':1-54', restraint_wt=200.0,
> >> /
> >> &ewald
> >> /
> >> [stumusii.eric2 min-eqb-prod]$ cat min2.in
> >> minimize structure
> >> &cntrl
> >> imin=1,maxcyc=50000, ncyc=5000,iwrap=1,
> >> ntb=1, cut=8, ntwx=500, ioutfm=1,
> >> /
> >> &ewald
> >> /
> >>
> >>
> >> Production:
> >> CZRA : equilibration
> >> &cntrl
> >> nstlim=100000000, dt=0.002,ntx=7,irest=1,ntpr=1000,ntwx=10000,
> >> tempi=300.0, temp0=300.0, ntt=3, imin=0, ntwv=-1,
> >> ntb=2, cut=8,ig=-1,ntwr=1000,
> >> pres0 = 1.0, ntp = 1,iwrap=1,
> >> taup = 2.0, ig=-1,
> >> ntc=2, ntf=2, gamma_ln = 2.0,
> >> ioutfm=1,
> >> /
> >> &ewald
> >> /
> >>
> >>
> >> thank you!
> >> ________________________________________
> >> From: Daniel Roe [daniel.r.roe.gmail.com]
> >> Sent: Wednesday, October 29, 2014 10:20 AM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Imaging
> >>
> >> Hi,
> >>
> >> All imaging routines ('autoimage', 'image') will correctly place atoms
> >> inside a unit cell unless your box coordinates (used to create the
> >> unit cell vectors) are not right for some reason, such as trying to
> >> image after rms-fitting.
> >>
> >> Without a better description or example of your problem with
> >> 'autoimage' I can't begin to help with that. However, I can tell you
> >> that a 'center' command following an imaging command, e.g.:
> >>
> >>> image center :1-77562 bymask familiar
> >>> center :1-2
> >>
> >> can definitely shift atoms outside the box - any action that modifies
> >> coordinates after an imaging command can. Typically you center first,
> >> then image (this is what 'autoimage' does internally). If you had a
> >> 'center' command following 'autoimage' this would do the same thing.
> >>
> >> If you can give a more complete description of your issue I may be
> >> able to help further.
> >>
> >> -Dan
> >>
> >> PS - As always, make sure you're using the latest version of cpptraj (14.09).
> >>
> >>> image center :1-77562 bymask familiar
> >>> center :2-3
> >>> image center :1-77562 bymask familiar
> >>> center :3-4
> >>> image center :1-77562 bymask familiar
> >>> center :1-5
> >>> image center :1-77562 bymask familiar
> >>> center :5-6
> >>> image center :1-77562 bymask familiar
> >>> center :6-7
> >>> image center :1-77562 bymask familiar
> >>> center :7-8
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
\-/ Professor Thomas E. Cheatham, III
-/- Department of Medicinal Chemistry, College of Pharmacy
/-\ Director, Center for High Performance Computing, U of Utah
\-/
-/- tec3.utah.edu
http://www.chpc.utah.edu/~cheatham
/-\ SKH-4914 (801) 587-9652; FAX: (801) 585-6208
\-/ INSCC-410 (801) 585-6318; FAX: (801) 585-5366
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Received on Thu Oct 30 2014 - 14:00:02 PDT
