Thanks Sushil
On Mon, Sep 6, 2010 at 12:37 PM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> shape of water box is badly disturbed ? What do u mean by this ? I think u
> saw water molecules running our of the box, so there is nothing wrong in
> this. For periodic boundary conditions (ntb=1 or ntb=2), you can use
> variable "iwrap=1" to keep all particles in the same periodic box. The box
> is not really changing shape/size, problem is that without iwrap=1, the
> waters are diffusing out of the initial box and not being re-imaged back on
> the other side. you can do image of or trajectory and have a look in the
> proper shape.
>
> ..S
>
> On Mon, Sep 6, 2010 at 8:17 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
>
> > Hi All,
> > During the heating up of system using following script, the shape of
> water
> > box is badly disturbed. I am using TIP3P was water type and cubic water
> > box. Even after the heating step, the protein is well inside the waterbox
> > only the shape of waterbox is badly disturbed.
> >
> > Heating up the system equilibration stage 1
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > ntb = 1,
> > cut = 10.0,
> > ntr = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 1.0,
> > nrespa=2,
> > nstlim = 100000, dt = 0.002,
> > ntpr = 100, ntwx = 100, ntwr = 1000,
> > /
> > Keep Protein fixed with weak restraints
> > 10.0
> > RES 1 122
> > END
> > END
> >
> > My question is "shall I continue to the next step with the same system or
> > shall I re-frame the waterbox around the protein?"
> >
> >
> > Hirdesh
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Received on Mon Sep 06 2010 - 03:00:03 PDT
