[gmx-users] density of the bilayer

[Xavier Periole]

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

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