[gmx-users] density of the bilayer

[Xavier Periole]

On 12 Nov 2008 11:41:54 -0000
  "minnale " <minnale_gnos at rediffmail.com> wrote:
>  
> Thanks for your reply,
> In case of water density, starting of the water density will be for some 
>time should come straight line in the graph later gradually reducing and goes 
>to zero towards centre of the bilayer again it increases and stop going the 
>water density. 
> 
> but in my case starting water density itself reducing gradually instead of 
>coming straight line for while.
> is my opinion wrong?
Ok there you seem to be right.

Do you actually do the density only on water? You should give an index to
g_density and choose from it the water or something else.

Is your system centered? I mean the bilayer in the center of the z axis and
therefore the water distributed on both sides.

Do you actually have enough water solvating your balayer and therefore
showing this plateau value before the decrease?

XAvier

> 
> how actally I should get the water density plot of the bilayer?
> any suggestions would be appreciated
> 
> thanks in advance
> 
> On Wed, 12 Nov 2008 Xavier Periole wrote :
>>On 12 Nov 2008 11:13:51 -0000
>>  "minnale " <minnale_gnos at rediffmail.com> wrote:
>>>  Hi users, Intially I have run the simulation of the bilayer for 5ns then 
>>>extended this to 20ns. When analyse density of the bilayer by considering 
>>>trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc 
>>>its showing almost same density values how come it is possible?
>>I do not see the same values! They seem to fluctuate!
>>What would be so wrong in having similar values? Looks good to me!
>>>the command line is  g_density -f 5ns.xtc/20ns.xtc -s em.tpr -d z -o 
>>>5ns_den.xvg/20ns_den.xvg
>>>
>>>density output values at 5(coulm 1 and 2) and 20ns(column 3 and 4) 
>>> 5ns_den.xvg                     20ns_den.xvg
>>>          0           916.865    0                 869.8
>>>    0.113182          886.892    0.114679          840.058
>>>    0.226364          840.479    0.229359          793.811
>>>    0.339547          782.509    0.344038          736.194
>>>    0.452729          718.799    0.458717          667.985
>>>    0.565911          652.112    0.573397          589.507
>>>    0.679093          576.481    0.688076          509.389
>>>    0.792275          501.502    0.802755          437.914
>>>    0.905457          423.993    0.917435          374.713
>>>     1.01864          346.635    1.03211          314.386
>>>     1.13182           266.88    1.14679          247.738
>>>       1.245           195.44    1.26147          173.424
>>>     1.35819          123.363    1.37615          107.955
>>>     1.47137          68.3216    1.49083          51.0066
>>>     1.58455          34.0154    1.60551          21.3937
>>>       --               --        --               --       -- 
>>>              --        --               --
>>>       --               --        --               --
>>>         any comments would be appreciated
>>>
>>>Thanks in advance                                          
>>
>>-----------------------------------------------------
>>XAvier Periole - PhD
>>
>>- Molecular Dynamics Group -
>>Computation and NMR
>>University of Groningen
>>The Netherlands
>>-----------------------------------------------------

-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------