I have a minimization run previous to this, and I set up the ipol to a default 1. So how should I equilibrate the system with non polirizable potentials? How much is minimized?
The minimization is now resulting in this
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -2.8320E+05 2.3084E+06 3.2614E+07 HW 112
BOND = 0.0043 ANGLE = 0.0113 DIHED = 0.0000
VDWAALS = 14.4210 EEL = 3141.9935 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
EPOLAR = -286353.0043
Dipole convergence: rms = 0.455E+04 temperature = 0.00
NSTEP ENERGY RMS GMAX NAME NUMBER
51 -2.4814E+07 8.9139E+08 1.2598E+10 HW 112
BOND = 0.0043 ANGLE = 0.0113 DIHED = 0.0000
VDWAALS = 14.4204 EEL = 8934.3235 HBOND = 0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
EPOLAR = *************
Dipole convergence: rms = 0.396E+06 temperature = 0.00
Thanks for any help you can give
________________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Monday, September 14, 2015 12:08 AM
To: AMBER Mailing List
Subject: Re: [AMBER] What is wrong with the minimization?
On Mon, Sep 14, 2015, Huggins, Esther, C wrote:
>
> I'm trying to resolve some issues with the minimization ...
>
>
> Heating of 1M NaNO3 STAGE 1
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=4000000, dt=0.0005,
> cut=4.0,
Ouch....you can't use such a short cutoff! Use the default value of 8.
You should be able to use a dt value of 0.001 or 0.002, once you start getting
a stable simulation.
> ntf=2,ntc=2,
> ntt=3, gamma_ln=1.0,
> tempi=0.0, temp0=100.0,
> ntpr=50, ntwx=50,
> ntb=1,
> iwrap=1, ipol=1, ig=-1
If you are new to Amber, use a non-polarizable potential first (ipol=0).
Equilibrate the system with non-polarizable potentials, then you try
polarizable ones.
Carry out trial runs with ntpr=1, nstlim=100; use just the serial version
(not the parallel version). It looks like your starting coordinates for
MD have not been minimized (or minimized enough).
....good luck....dac
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Received on Mon Sep 14 2015 - 07:30:03 PDT
