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 - 00:30:03 PDT
