Re: How to confirm water box is big enough?

From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Tue Mar 30 2010 - 15:53:46 CDT

----- "Jin Liu" <jliunih_at_gmail.com> wrote:

| From: "Jin Liu" <jliunih_at_gmail.com>
| To: "David Tanner" <guacamoleo_at_gmail.com>
| Cc: namd-l_at_ks.uiuc.edu
| Sent: Tuesday, March 30, 2010 4:44:26 PM GMT -05:00 US/Canada Eastern
| Subject: Re: namd-l: How to confirm water box is big enough?
|
| Thank you very much David. I can tell from the VMD that there is no
| direct interact between protein and its image. But is there a way that
| I could measure the shortest distance between protein and its images
| during the simulation to make sure? I need to address it to a
| reviewer's comment. Thank you very much.

Depending on the box you used and its orientation, you could presumably do it with CHARMM by analyzing your trajectory. I guess you can do it with VMD too, but I am not very familiar with the image facility tools available there.

Dimitar
 
|
|
|
| On Tue, Mar 30, 2010 at 4:13 PM, David Tanner < guacamoleo_at_gmail.com >
| wrote:
|
|
|
| One thing, and there may be several others, you must test is to verify
| that the protein doesn't directly interact with itself. This means
| that no atom in the protein should ever be within CUTOFF of any atoms
| in any periodic image.
|
|
|
|
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| David E. Tanner
| Theoretical and Computational Biophysics Group
| 3159 Beckman Institute
| University of Illinois at Urbana-Champaign
| 405 N. Mathews
| Urbana, IL 61801
| http://www.linkedin.com/in/davidetanner
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
|
| On Mar 30, 2010, at 2:29 PM, Jin Liu wrote:
| Hi,
|
| I did a few MD simulations with the the minimum distance from the
| protein to the edge of the water box as 10 angstrom. The simulations
| ran smoothly without any problem. I am wondering what I could do to
| confirm the water box is big enough? Should I measure the distance
| between the protein and its image in the other boxes during the
| simulation? Or what else can I do to convince people that the water
| box is not too small?
|
|
| Thank you very much.
|
|
| Best regards,
|
|
| Jin

-- 
========================================================
Dimitar V Pachov
PhD Candidate
Physics & Biochemistry Department     Phone: (781) 736-2326
Brandeis University, MS 057           Email: dpachov_at_brandeis.edu
========================================================

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