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
> Member Research Staff
> LeadInvent Technologies Pvt.Ltd
> Biotech Centre, University of Delhi
> South Campus, Benito Juarez Road,
> New Delhi, Pin 110021
> Email- sunita.leadinvent.com
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 29 2011 - 06:00:05 PDT
