If the structure was determined by homology modeling then I would suggest to
be careful and focus in the minimization and equilibration procedure.
Definitely it will also depend in the homology used during the modeling so
allow sufficient run during the each step of minimization and eventually
check energy and rmsd.
sm :-)
On Mon, Mar 15, 2010 at 9:07 AM, Pallavi Mohanty
<pallavipmohanty.gmail.com>wrote:
> Yea its a homology modelled one.But do you mean to say i can still run my
> simulation.
>
> On Mon, Mar 15, 2010 at 1:14 PM, Sushil Mishra <sushilbioinfo.gmail.com
> >wrote:
>
> > Hi,
> >
> > I cant see any particular problem with input parameters. I think this may
> > be
> > due to some twist in initial crystal structure. If you think your
> starting
> > structure is a good one, it is most try to quilibrate with restraints on
> > the
> > coordinates. Once the system is equilibrated at 298K, you can remove the
> > constraints, but be sure that your structure is still pretty close to the
> > starting one.
> >
> > Vlimit errors are not necessarily something to worry about, but you
> should
> > certainly check that your structure is still in good shape.
> >
> > Good Luck
> >
> > SM :-)
> >
> >
> > On Mon, Mar 15, 2010 at 12:59 PM, Pallavi Mohanty <
> > pallavipmohanty.gmail.com
> > > wrote:
> >
> > > Hello all,
> > > Running equilibration and taken below mentioned parameters
> > > imin = 0,
> > > ntx = 1,
> > > ntb = 1,
> > > scnb=2, scee=1.2,
> > > dielc=2,
> > > cut = 16,
> > > ntc = 2,
> > > ntf = 2,
> > > tempi = 0.0,
> > > temp0 = 300.0,
> > > ntt = 3,
> > > gamma_ln = 1.0,
> > > nstlim = 100000, dt = 0.001,
> > > ntpr = 100, ntwx = 100, ntwr = 1000
> > > /
> > > after each run its giving an output as NSTEP = 800 TIME(PS) =
> > > 0.800 TEMP(K) = 498.77 PRESS = 0.0
> > > Etot = 14702.7141 EKtot = 45245.1250 EPtot =
> > > -30542.4109
> > > BOND = 7777.3361 ANGLE = 11167.4726 DIHED =
> > > 4271.4812
> > > 1-4 NB = 1833.3012 1-4 EEL = 5701.1018 VDWAALS =
> > > -3104.8477
> > > EELEC = -58188.2561 EHBOND = 0.0000 RESTRAINT =
> > > 0.0000
> > > Ewald error estimate: 0.5280E-05
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > >
> > > vlimit exceeded for step 800; vmax = 36.1486
> > > vlimit exceeded for step 801; vmax = 24.1706
> > > vlimit exceeded for step 802; vmax = 259.5763
> > > vlimit exceeded for step 803; vmax = 24.2270
> > > vlimit exceeded for step 804; vmax = 21.3719
> > > vlimit exceeded for step 805; vmax = 22.9561
> > > Do revert me where i am lacking.Thanks in advance
> > >
> > >
> > > --
> > > Regards,
> > >
> > > Pallavi Mohanty
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> > >
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> >
>
>
>
> --
> Regards,
>
> Pallavi Mohanty
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Received on Mon Mar 15 2010 - 02:30:05 PDT
