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
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Received on Fri Apr 29 2011 - 05:00:04 PDT
