Hi Dr Roe,
Thanks for you prompt response.
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.
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)
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Received on Wed Oct 29 2014 - 09:00:03 PDT
