Hi,
In ptraj.in you have way too many 'image' and 'center' commands - what
were you trying to do? Also as I said before, your final 'center
:1-54' command will probably end up shifting some molecules out of the
box anyway.
In ptraj1.in you are not using 'autoimage', so the results may not be
what you intended. The 'image' command makes no effort to keep solute
molecules together like 'autoimage' does.
In ptraj2.in you also have way too many 'image' and 'center' commands,
but then you have an 'autoimage' command at the end which renders all
of those previous commands pointless anyway; i.e. instead of all the
'image' and 'center' commands just use one 'autoimage' command. Was
there a problem with the trajectory that was output from this cpptraj
input?
In ptraj3.in you have 'image' before 'center'. Also the first 'trajin'
command is misspelled "trajjin".
What I recommend is trying something like this:
trajin prod.netcdf
autoimage
trajout prod.imaged.nc
And see if that works for you.
-Dan
On Wed, Oct 29, 2014 at 10:22 AM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
> Here is one other ptraj.in file that i have used.
>
> 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
>>
>> _______________________________________________
>> 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
Received on Wed Oct 29 2014 - 14:00:02 PDT
