Hi Dr .Roe,
I have attached three different ptraj.in files that i have attempted to use with differing results for the imaging in VMD as described in my previous email/
Thank you,
Sylvester
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Wednesday, October 29, 2014 10:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Imaging
Hi,
On Wed, Oct 29, 2014 at 9:38 AM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> My system consists of molecules in a solvent (different water models) with or without ions.
>
> After i try the different centering or imaging techniques as i mentioned, i make the following observations:
>
> When i look at some of the trajectories in VMD i can either see the water box shaking violently (rotating around the center) while in other simulations i can see the molecules am interested in at the edge of the box on opposite sides as you would expect if the centering had not worked.
The first symptom sounds to me like RMS-fitting was performed on the
trajectory. RMS-fitting a trajectory with PBC effectively invalidates
the unit cell vectors since the coordinates are rotated into a new
coordinate system; in other words, once you rms-fit a trajectory with
PBC imaging can no longer be effectively performed. Up-to-date
versions of cpptraj print a warning to this effect.
What I would really need to see is all of your entire cpptraj inputs,
unless the problems you are having are with your unaltered
trajectories (i.e. the trajectories straight from the simulation).
-Dan
>
>
> These are the conditions i used for minimisation-equilibratiion-production
>
> Equilibration 1:
> CZRA : equilibration
> &cntrl
> nstlim=100000, dt=0.002,ntx=1,irest=0,ntpr=500,ntwr=5000,ntwx=5000,
> tempi=0, temp0=300.0, ntt=3, imin=0,
> ntb=1, cut=10, iwrap=1,
> 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
>
> _______________________________________________
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> 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)
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- application/octet-stream attachment: ptraj.in
- application/octet-stream attachment: ptraj1.in
- application/octet-stream attachment: ptraj2.in
Received on Wed Oct 29 2014 - 09:30:02 PDT
