On 14/08/2012 6:16 PM, Emanuel Birru wrote:
I am not sure whether a pressure coupling equilibration enlarges the specified
box size of the simulation :)
It can.
if the box size is not appropriate to maintain the pressure coupling the
simulation probably blow up instead of adjusting the box size to a bigger one.
Just as with shrinking, it depends on the coupling algorithm, the
timestep and how far from equilibrium the volume is.
Mark
For more info check the following links and consult with gromacs manual
http://www.gromacs.org/Documentation/Terminology/Equilibration?highlight=equilibration
http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling
Cheers,
EB
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Tuesday, 14 August 2012 6:08 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fw: box of simulation
Hi Emanuel,
Thank you very much from your response.
yes, my topology is correct.
It means that it isn't one problem and it is natural.yes?
This question is because of in the most of papers has been said that the box is
enlarged with equilibrium but my box become smaller!
Best Regards
Sara
----- Original Message -----
From: Emanuel Birru <emanuel.bi...@monash.edu>
To: 'mohammad agha' <mra...@yahoo.com>; 'Discussion list for GROMACS users'
<gmx-users@gromacs.org>
Cc:
Sent: Tuesday, August 14, 2012 12:06 PM
Subject: RE: [gmx-users] box of simulation
Hi Sara,
The number of molecules in your .gro file and .top file should be the same.
That means when you want to add 12000 solvent molecules, change the number of
solvent molecules in your topology file to 12000. The total number of your
solvent and solute molecules in you topology and coordinate files should be the
same.
When you do constant pressure equilibration it is normal to see your box
shrinking as long as you are pretty sure that the number of molecules in the
box is correct. I you do need no change on the size of the box, run a constant
volume equilibration.
Cheers,
EB
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Tuesday, 14 August 2012 5:27 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] box of simulation
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950) it means that I should
enlarge the box to place all of solvent molecules into that.
But when the system equilibrium with running pr.mdp, box become smaller till
13.9*13.9*13.9!!!
What should I do with this problem?
Is it a problem?!
Thank you very muchin advance.
Best Regards
Sara
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