[gmx-users] about equilibrium

mohammad agha mra_bu at yahoo.com
Mon Oct 15 18:37:40 CEST 2012

Dear Justin,

The previous problems was as is following:

> Dear GROMACS Users,
> I asked this question before but I don't understand it!
 I placed several materials in my box of simulation for example box with
 6nm*6nm*6nm and my materials are not placed in the smaller box but when
 I equilibrate my system, the box became smaller and temperature and 
pressure also equilibrate. my question is: is my system and equilibrate 
mistake, because of reach to smaller box? Is there equilibriums with 
reach to smaller box?

What do you mean by "my materials are not placed in the smaller box"?

If a box compresses, it is because the initial configuration was incompatible 
with the desired equilibration conditions and it contracted produce the desired 
quantity (likely pressure).


> Dear Justin,
> "my materials are not placed in the 
smaller box" means if I select box with dimensions 5.99 nm, space is low
 and insufficient for my molecules! but after equilibrate the box become

Please define what you mean here.  You start with a 6-nm 
cubic box.  How small does it get?  Are the box vectors trending 
downward, or do they converge?  What is the change in density, and is it

> According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural?

 depends on the magnitude of the change.  Compression indicates that the
 pressure (and thus density of the system) was not at the desired value 
and the system is contracting.  The manner in which the contraction 
occurs (magnitude, speed) is the deciding factor as to whether or not 
there is a problem.


> Dear Mark,
> > May I know your idea about cause of my doubt, Please?

As I said yesterday:

> At least one of your volume, contents or model physics are not 
> consistent with the others, but only you can say which. 

Since only you know anything about your volume, contents and model 
physics, or that of the work you think you should be replicating, we 
can't help at the moment. See previous comment about relevant 
information :-)


> 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: Friday, October 5, 2012 9:34 AM
> Subject: Re: [gmx-users] equilibrium for box of simulation
> On 5/10/2012 3:55 PM, mohammad agha wrote:
>> Dear Justin,
>> Thank you very much.
>> So, decreasing of box dimensions is not bad, if all thing process natural, yes?
 The cause of my doubt was because of in the most of articles was said 
for example " we select box with dimensions 10nm that after equilibrium 
was converted to 11nm" and I didn't see the report of decreasing of box 
dimensions! May I know your idea about it, Please?
> Following a 
published method closely and observing an opposite result is a cause for
 concern. You have to judge "closely," however. You should have said 
earlier this was one of your reasons for doubt, rather than leave us to 
guess. The quality of the help you might receive is often in direct 
proportion to the quantity of relevant information you give in asking 
for it.
> Mark

----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, October 15, 2012 7:50 PM
Subject: Re: [gmx-users] about equilibrium

On 10/15/12 12:11 PM, mohammad agha wrote:
> Dear Justin,
> Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject "equilibrium for box of simulation". When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct?

Please provide a link to the previous thread.  I read hundreds of posts per 
week; I don't recall this one.  A sequence of commands would also be helpful 
here, as I cannot clearly envision what you are describing.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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