Re: [AMBER] constant pH equilibration confusion

From: Sangita Kachhap <>
Date: Sun, 20 Jun 2010 01:29:26 +0530 (IST)

Ya I have seen the tutorial for simulation of DNA in implicit solvant
there is relaxing the DNA before MD simulation at tempi = 300.0, temp0 = 300.0.
But actualy in one of the reply of my mail I got about heating and equilibration
so thats why I have confusion.
For constant pH simulation I am donig the following step is it correct or not?
a)minimization of hydrogen only (by mistake I my earlier mail I have wrote
  that i hvae apply restraint on hydrogen).
b)minimization of whole system

2)heating (now which I will not do) and equilibration at tempi = 300.0, temp0 =

3)production run.

>> Now I have to euqilibrat it with heating 0 - 300K.
> Have you looked at the tutorials?
> Bill
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Sangita Kachhap

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Received on Sat Jun 19 2010 - 13:00:03 PDT
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