Thank you very much for your comments!
Yan
On Mon, Jul 26, 2010 at 10:46 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> be very careful if you plan to use explicit ions with GB. it was discussed
> on this list recently.
> there is also significant local expertise on continuum solvation at UCSD-
> talk to those people and see what they think about this.
> look at the positions of your Na+ and see where they are going.
>
>
> On Mon, Jul 26, 2010 at 1:42 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am trying to simulate 4 large molecules (totally 14000 atoms) with 160
> > negative charges (balanced by Na+).
> > I setup the .prmtop and .inpcrd files. Plan to minimize the system energy
> > first in vac, then with gb, then simulate the system with gb.
> >
> > However during my first minimization in vac, the totally energy keeps
> > positive (although decreasing). May I know if this is normal? Thanks.
> >
> >
> > Below are the last steps:
> >
> >
> ************************************************************************************************
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 4900 4.2524E+04 6.1255E-01 1.5029E+01 Na+ 13192
> >
> > BOND = 3072.5966 ANGLE = 5996.4700 DIHED =
> > 21717.1678
> > VDWAALS = -4816.7280 EEL = -2387.7248 HBOND =
> > 0.0000
> > 1-4 VDW = 9620.1746 1-4 EEL = 9321.6567 RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 4950 4.2483E+04 5.0476E-01 1.1085E+01 Na+ 13175
> >
> > BOND = 3064.7886 ANGLE = 5976.9772 DIHED =
> > 21720.5243
> > VDWAALS = -4815.9956 EEL = -2408.2766 HBOND =
> > 0.0000
> > 1-4 VDW = 9620.5387 1-4 EEL = 9324.8584 RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 5000 4.2580E+04 5.7094E-01 1.2015E+01 Na+ 13175
> >
> > BOND = 3058.8158 ANGLE = 5958.4449 DIHED =
> > 21725.4094
> > VDWAALS = -4818.3656 EEL = -2294.1242 HBOND =
> > 0.0000
> > 1-4 VDW = 9621.5499 1-4 EEL = 9328.4365 RESTRAINT =
> > 0.0000
> >
> >
> ************************************************************************************************
> > Regards,
> > --
> > Yan Gao
> > Jacobs School of Engineering
> > University of California, San Diego
> > Tel: 858-952-2308
> > Email: Yan.Gao.2001.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Mon Jul 26 2010 - 11:30:07 PDT
