AMBER Archive (2009)
Subject: Re: [AMBER] box problem
From: Nancy (nancy4619_at_163.com)
Date: Mon Aug 17 2009 - 22:02:21 CDT
Thank you Ashish Runthala for your kindness.Do you mean i should set two boxes ,one is for nanotubes ,the other is for water?
在2009-08-16，"Ashish Runthala" <ashish.runthala_at_gmail.com> 写道：
>See, as there are 4 tubes, shown in 2 lines, see it as a matrix of 2x2.
>As per your information, both the diameters are same.
> X Y Z
>Line 1: 15 7 27
>Line 2: 15 7 27
>(All are in Å units)
>Water is 10Å thick, 20, 17, 10 in X,Y,Z.
>I guess, do the following steps.
>1. Set a box with dimensions, 15 7 27. This dimension wont allow any
>interstitial space, to solve your first problem.
>2. As water TIP3PBOX unit is considered 2.8Å in length, solvate till
>the 10Å, which will add water molecules.
>3. Now check the confirmation.
>4. If it is correct, do step 5. Else relax the structure with some 500 cycles.
>5. Apply another box of 20, 17,10 finally and apply periodic volume
>from there onwards.
>Do let me know, about it.
>Faculty Division III,
>Assistant Lecturer, Biological Sciences,
>Birla Institute of Technology and Science,
>Pilani, Rajasthan- 333031
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