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

[Ali Alizadeh]

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?

> 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?

4- I have three types of molecules, There is one layer of water
between two same layers.

      pbc for all of directions!