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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Apr 30, 2011, at 10:00 AM, sunita gupta <sunita.bio.gmail.com> wrote: > 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 >>> >> _______________________________________________ >> 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Apr 30 2011 - 02:00:03 PDT