Justin Lemkul jalemkul at vt.edu
Mon Oct 15 20:24:17 CEST 2012

```I didn't see anything inherently wrong with your previous observations, so I
suspect your new approach is probably fine.  There are several ways to do just
about anything; you just need to find one that works to your satisfaction and
represents a reasonable model of whatever you're trying to simulate.

-Justin

On 10/15/12 12:37 PM, mohammad agha wrote:
> 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).
>
> -Justin
>
>> 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
>   small.
>
> 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
>   acceptable?
>
>> According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural?
>>
>
> That
>   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.
>
> also,
>
>
>> Dear Mark,
>>
>>
>
> 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 :-)
>
> Mark
>
>>
>> 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
>> 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
> 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>
> Cc:
> 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?
>>
>
> 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
>

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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