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
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>
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Received on Mon Jul 26 2010 - 11:00:05 PDT
