Hello Carlos,
Again I did the centering as well as imaging using ptraj command :
*center:1-368
image center familiar*
and even visualized the trajectory ...everything seems perfect...and solvent
is not moving far from the central box.
I again ran the minimization using Amner10...nd got the same output pasted
earlier..
This time also tried with Amber11 and prepared the min.in file based on
trajene.in (amber11/test/trajene_box/). Here the things are running fine.
Below is the min.in file
&cntrl
imin = 5, ntx = 1,
ntt = 1, tautp = 1.0, temp0 = 300.0, tempi = 300.0,
ntc = 2, ntf = 1, ntb = 2,
ntp = 1, taup = 1.0,
ntwx = 1, ntwe = 0, ntwr = 1, ntpr = 1, ioutfm = 0,
cut = 12.0, iwrap = 1,
/
As Amber11 is supporting the PBC condition , will it be ok if I use Amber11
for minimizing the trajectory and further use it for normal mode calculation
using Amber10?
Guide me if I am doing anything wrong.
Many thanks.
On Fri, Apr 29, 2011 at 6:26 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> you said centering has been done- but did you image? it's possible that if
> you didn't have imaging on in the MD, that the solvent has moved far from
> the central box. visualize the trajectory before postprocessing to make
> sure
> you know what you're analyzing.
> On Fri, Apr 29, 2011 at 8:40 AM, sunita gupta <sunita.bio.gmail.com>
> wrote:
>
> > If I am using ntb = 1, I am getting an error "IMIN=5 does not support
> > periodic boundaries (ifbox>0, ntb>0)", hence I uesd ntb =0
> >
> > On Fri, Apr 29, 2011 at 5:56 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > If water and stuff is present, do you really want to be using ntb == 0?
> > If
> > > you just use ntb = 1, then you should get the necessary behavior
> without
> > > having to center/image (moreover, you actually treat the long-range
> > > electrostatics properly).
> > >
> > > HTH,
> > > Jason
> > >
> > > On Fri, Apr 29, 2011 at 1:42 PM, sunita gupta <sunita.bio.gmail.com>
> > > wrote:
> > >
> > > > Yeah, water is present and centering of mdcrd file has been done
> using
> > > > ptraj.
> > > >
> > > > Thanks
> > > >
> > > > On Fri, Apr 29, 2011 at 5:09 PM, Adrian Roitberg <
> roitberg.qtp.ufl.edu
> > > > >wrote:
> > > >
> > > > > I am assuming this was done with a water box ?
> > > > > Try centering/imaging your molecule/box before using imin=5
> > > > >
> > > > > On 4/29/11 1:36 PM, sunita gupta wrote:
> > > > > > Hello Everyone,
> > > > > >
> > > > > > I am having 5ns mdcrd file and I want to minimize it further with
> > > > imin=5
> > > > > for
> > > > > > maxcyc=5000. But here I am getting the mdcrd file having only one
> > > frame
> > > > > and
> > > > > > no rst file.
> > > > > > The out file shows that it ran for one step, Can anyone help me
> > with
> > > > this
> > > > > > error? I am using Amber10.
> > > > > > *min.in file (minimization input file)*
> > > > > > &cntrl
> > > > > > imin = 5,
> > > > > > maxcyc = 5000,
> > > > > > ncyc = 2000,
> > > > > > ntb = 0,
> > > > > > ntr = 0,
> > > > > > cut = 12, ntpr = 1, ntwx = 1,
> > > > > > nmropt=0,
> > > > > > /
> > > > > > *Min.out file is pasted below:*
> > > > > >
> > > > > > Maximum number of minimization cycles reached.
> > > > > > FINAL RESULTS
> > > > > > NSTEP ENERGY RMS GMAX NAME
> > > > > NUMBER
> > > > > > 5000 -8.7965E+04 3.1104E+00 8.1496E+01 HB2
> > 1765
> > > > > >
> > > > > > BOND = 13550.5326 ANGLE = 985.3458 DIHED =
> > > > > > 3417.9826
> > > > > > VDWAALS = 27007.4725 EEL = -149685.0349 HBOND =
> > > > > > 0.0000
> > > > > > 1-4 VDW = 1250.1481 1-4 EEL = 15508.2819 RESTRAINT =
> > > > > > 0.0000
> > > > > > minimization completed, ENE= -.87965271E+05 RMS= 0.311043E+01
> > > > > > minimizing coord set # 2
> > > > > > Frac coord min, max: -1202863.84373385
> 1202865.00693183
> > > > > > The system has extended beyond
> > > > > > the extent of the virtual box.
> > > > > > Restarting sander will recalculate
> > > > > > a new virtual box with 30 Angstroms
> > > > > > extra on each side, if there is a
> > > > > > restart file for this configuration.
> > > > > > SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> > > > > > Atom out of bounds. If a restart has been written,
> > > > > > restarting should resolve the error
> > > > > >
> > > > > > *The command used is:* mpirun -np 4 /opt/apps/amber10/exe/sander
> -O
> > > -i
> > > > > > min.in -o LI4_min.out -p pro_LI4.top -c pro_LI4.crd -y
> > LI4_5ns.mdcrd
> > > > -r
> > > > > > LI4_min.crd -x LI4_min.mdcrd
> > > > > >
> > > > >
> > > > > --
> > > > > Dr. Adrian E. Roitberg
> > > > > Associate Professor
> > > > > Quantum Theory Project, Department of Chemistry
> > > > > University of Florida
> > > > >
> > > > > on Sabbatical in Barcelona until August 2011.
> > > > > Email roitberg.ufl.edu
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > --
> > > > SUNITA GUPTA
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > --
> > SUNITA GUPTA
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
--
SUNITA GUPTA
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Received on Sat Apr 30 2011 - 01:30:02 PDT
