On 12 Nov 2008 11:41:54 -0000
"minnale " <[EMAIL PROTECTED]> 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 " <[EMAIL PROTECTED]> 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
-----------------------------------------------------
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