[gmx-users] density of the bilayer

[minnale]

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?

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
>-----------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081112/c54b6dfd/attachment.html>