I did try starting MD again and it does work but the minimization doesn't go
to completion again.
When I start again it completes 100 steps out of 2000 steps.
Does this mean it is already minimizer? Would it be a good
idea to proceed to equilibration with this structure?
Thanks,
Chayya B.
On Fri, Aug 25, 2017 at 2:10 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> With 10K dynamics, you will find a lower minimum, I'll bet. Try ignoring
> it, and see if you have any problems starting md.
>
> Bill
>
>
> On 8/24/17 11:05 PM, Chayya Bhargac wrote:
> > Dear Amber users,
> >
> >
> > I am trying to perform a minimization for a system set up with POL3
> > water box and ff02 force fields. It has 24 Ca2+ and 20 Cl- ions.
> >
> > While performing a restrained minimization with the code below, I get a
> > LINMIN error. From previous posts in the mailing list, people have
> > continued with their simulations despite the error. But in my case, the
> > minimization stops completely. The minimization which has 4000 steps,
> stops
> > in 200 steps. If this is because of bad contacts, what can I do to remove
> > it? Is there any way to proceed after this?
> >
> >
> > Minimization code:
> >
> > Minimization with Cartesian restraints for the solute
> >
> > &cntrl
> >
> > imin=1, maxcyc=400, ncyc=100, ntc=2, ipol=1,
> >
> > ntpr=50, ntr=1
> >
> > $end
> >
> > Group input for restrained atoms
> >
> > 500.0
> >
> > RES 1 172
> >
> > END
> >
> > END
> >
> >
> > Error:
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> >
> > 200 -3.5241E+05 1.9021E+01 1.6012E+02 HD12 53
> >
> >
> > BOND = 69.5447 ANGLE = 457.3107 DIHED =
> > 1518.5396
> >
> > VDWAALS = 86424.7986 EEL = -358147.2457 HBOND =
> > 0.0000
> >
> > 1-4 VDW = 690.4683 1-4 EEL = 8524.4425 RESTRAINT =
> > 397.4833
> >
> > EPOLAR = -92346.4873
> >
> > EAMBER = -352808.6287
> >
> > Dipole convergence: rms = 0.560E-01 temperature = 0.00
> >
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> > ***** REPEATED LINMIN FAILURE *****
> >
> >
> >
> >
> > Thank you,
> > Chayya B.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Aug 25 2017 - 08:30:05 PDT
