[gmx-users] box of simulation

[mohammad agha]

Dear Mark,

Thank you very much from your help.

I used from genbox to place solvent molecules. my question is : In the NPT ensemble, for equilibrium, may the box become smaller than definite sizes before equilibrium(for example 2nm become smaller) and if yes, why haven't been placed molecules in the box smaller before equilibrium initially and they need to more size and during equilibrium become smaller?

Best Regards
Sara




----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, August 14, 2012 1:01 PM
Subject: Re: [gmx-users] Fw: box of simulation

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-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
>
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