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
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Received on Fri Apr 29 2011 - 06:00:03 PDT
