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 - 01:30:03 PDT
