On Jan 26, 2011, at 4:39 PM, John S wrote:
> Hi ,
>
> If I use packmol to construct the box of polymer with solvent , does AMBER
> work well with this.
>
> Thanks
> John
You will probably have to set a box considerably larger than what
packmol thinks you need. The reason is that you will get VDW overlap at
the edges of the boxes you construct. Constant pressure dynamics is
your friend (it is needed to equilibrate the density). If NPT dynamics
continually bombs, increase the size of the initial box manually until
it runs. Plot the density so you can convince yourself it is
equilibrated.
Bud Dodson
>
> On Wed, Jan 26, 2011 at 3:04 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> PS
>>
>>> It constructs the solvated sample .Is there way of controlling how many
>>> molecules of solvent molecule I want to add.
>>
>> Maybe packmol (not in Amber) could do this, then loadpdb and setbox.
>>
>> Bill
>>
>>
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Wed Jan 26 2011 - 15:30:05 PST
