[gmx-users] equilibrium for box of simulation

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 5 08:18:36 CEST 2012

On 5/10/2012 4:12 PM, mohammad agha wrote:
> Dear Mark,
> Yes, you're right. Excuse me, for this and thank you for your reminder.
> 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
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