[gmx-users] Fwd: I have a symmetric simulation box,

[Justin Lemkul]

On 10/18/12 6:15 AM, Erik Marklund wrote:
>
> 18 okt 2012 kl. 12.08 skrev Ali Alizadeh:
>
>> Dear All users
>>
>> 1- I have a symmetric simulation box but i can not produce a symmetric
>> number density result (number density vs. z direction(nm))
>>
>> My simulation box is orthorhombic. My boundary condition is pbc but i
>> don't perform any commands before final run for
>>
>> Preparation of simulation box(related to pbc) and Just, in my input
>> file(.mdp file) select  pbc xyz-option.
>>
>>      1- construction of simulation box with a software
>>      2- pdb2gmx for producing .gro and .top
>>      3- energy minimization
>>      4- nvt(it converged)
>>      5- npt(it converged)
>>      6- production of md(2 nano second)
>>

A simulation length of two nanoseconds is probably too short.  The files you 
emailed me off-list showed that your density plot was fairly normal, just rough. 
  Simulate longer, and perhaps discard some of the initial frames as 
equilibration (standard practice).

-Justin

>> 2- I don't locate the centre of masses. How can i  determine it?Is it necessary?
>>
>
> The center of mass is undefined for a periodic system.
>
>> --
>> Sincerely
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>

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

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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