[gmx-users] Re: gmx-users Digest, Vol 102, Issue 99

Justin Lemkul jalemkul at vt.edu
Wed Oct 17 01:35:16 CEST 2012

On 10/16/12 11:10 AM, Ali Alizadeh wrote:
> Dear Justin
> Thank you for your reply,
> On 10/16/12 7:55 AM, Ali Alizadeh wrote:
>> Dear All users
>> 1- When i use these commands for generating number density profile
>> I see completely different results(in z direction, length in z
>> direction is 8, number density versus of z)
>> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z -symm -center
>> It's trend is increasing(from z=0 to z=2 then decreasing(fall to zero,
>> z= 2-5) and then increasing(z=5-7.5)
>> g_density -f md.xtc -s md.tpr -dens number -o  dens8.xvg -d z
>> But in the case,It's trend is decreasing(z=0-2.5) then
>> increasing(suddenly to maximum, z=2.5-5) and then decreasing(z=5-8)
>      Justin wrote:
>             You're telling g_density to do two different things.  You
> got two different
>              results.  I don't see that as odd.
> 1- I don't know different between them , can you further explain?

If you don't understand the command line options, perhaps you should do a bit 
more background reading and testing to understand them.  In one command, you are 
symmetrizing and centering the system, in another you are not.  Different 
commands will lead to different output.  Images of the plots would be more 
useful than vague descriptions.

>> 2- Number density profile Should be symmetric?
>        Justin wrote:
>           Only if the system is symmetric.
> 2- My system is symmetric but unfortunately my number density results
> is not symmetric.
> 3- Can you help me for using correct command for results of number density?

In theory, your first command will produce the desired output.  I can offer no 
explanation as to why your symmetrical system does not appear to be symmetrical. 
  Are you using NPT?  Changes in the box dimensions can mess up box slices in 

> 4- I have three types of molecules, There is one layer of water
> between two same layers.
>        pbc for all of directions!

Seems like it should be symmetrical, assuming of course that there are an equal 
number of molecules on both sides of the central layer.



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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