[gmx-users] box of simulation

[mohammad agha]

Thank you very much.

Best Regards
Sara



----- Original Message -----
From: Emanuel Birru <Emanuel.Birru at monash.edu>
To: 'mohammad agha' <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, August 14, 2012 12:46 PM
Subject: RE: [gmx-users] Fw: box of simulation

I am not sure whether a pressure coupling equilibration enlarges the specified box size of the simulation :) 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.

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-bounces at gromacs.org [mailto:gmx-users-bounces at 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.Birru at monash.edu>
To: 'mohammad agha' <mra_bu at yahoo.com>; 'Discussion list for GROMACS users' <gmx-users at 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-bounces at gromacs.org [mailto:gmx-users-bounces at 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

--
gmx-users mailing list    gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing list    gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists