Re: Sticking TIP4P water molecules AMBER

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Mon Dec 19 2011 - 04:58:13 CST

Hi Norman,

We do have some simulations running with the TIP4P-Ew + AMBER99SB (or
AMBER99SB-ILDN) combination with Langevin, and we haven't noticed any
obvious problems (yet ?). We are using 'NAMD CVS-2011-12-12 for
Linux-x86_64' + ambertools 10.

Nicholas

On Mon, 19 Dec 2011, Norman Geist wrote:

> Hi experts,
>
> I'm getting some strange behavior when simulating tip4p water using a
> thermostat. If I simulate without langevin, the water diffuses really fast,
> what is expectable. When using langevin, the water seem to compress a little
> and then sticks together as a whole bunch. There are long chains of the
> dummy atoms to hydrogens.
>
> It looks like the dummy atoms have very strong charges, or is this a usual
> behavior?
> Any ideas?
>
> Thanks in advance
>
> Norman Geist.
>

-- 
            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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