AMBER Archive (2004)

Subject: RE: AMBER: MD simulation : problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jul 11 2004 - 19:41:11 CDT

Dear Sachin,
 
If you are trying to observe the movement of the water molecules you are
unlikely to learn much bu having a water cap of jut 32 water residues. The
reason for this is that the outer water molecules of the cap has a
restraining force that acts to keep them as part of the water cap and so
stop them boiling off into vacuum. With only 32 water molecules in the cap a
large proportion are going to be restrained and so the movement of the water
molecules is going to be un-representative of a bulk system.
 
I'm not sure what you mean by the statement "I tried to run the simulation
with periodic boubdary conditions (cutoff 12.0) but the system just doesn't
go anywhere."
 
Are you implying it runs very slowly (what computer spec do you have and how
big is your system) or that something is wrong with the MD. Ideally if you
can afford it you want to run periodic boundary conditions with your entire
system solvated in a box of water. Typically you want a buffer size of at
least 10A around the entire protein. If you cannot afford such an expensive
calculation then try a solvent cap or implicit solvent but be aware of the
limitations. Especially with regard to things being restrained in the
solvent cap case.
 
I hope this helps.
All the best
Ross
 
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
sachin patil
Sent: 11 July 2004 08:08
To: amber_at_scripps.edu
Subject: RE: AMBER: MD simulation : problem

Hi Ross,
 Thank you for you suggestions. It really helps a lot.
 Actually, I have solvated my system with a water cap (32 water residues)
and I am trying to see the movement of the water molecules.
 I tried to run the simulation with periodic boubdary conditions (cutoff
12.0) but the system just doesn't go anywhere. So I switched to nonperiodic
conditions as mentioned
 in the Streptavidin Biotin tutorial.
 But my problem was that I was not sure whether I am correct in using
non-periodic
 conditions for my system.
  So my questions is how do one selectes whether he should use periodic or
non-periodic conditions for his system?
 
Thank you again
 
Regards
Sachin Patil
-----------------
Dept. of Medicinal & Biological Chemistry
University of Toledo, Toledo
Ohio 43606

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