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Re: electron density profiles via COOR HIST Z
rmv #7349 02/12/09 04:12 PM
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Quote:


! INTEGRATE TWICE
mantim chg integ
mantim chg integ
! WRITE RESULT





form the correl.doc

INTEgrate Q(z) = Integral(0-z) [ Q(z) dz ]

but in order to get the electrostatic potential
one said by integrating the poisson equation over the box in the z coordinate : Integral(0-z)dz´ Integral(0-z´)[ Q(z´´) dz´´ ]. I am wondering if the INTEGRATE TWICE as you suggested give the same meaning as electrostatic potential.

In addition, this parameter would be depend on the force field. I am right?

thank you

Re: electron density profiles via COOR HIST Z
beginner #7350 02/12/09 11:06 PM
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The double integral of the charge density across the membrane gives the dipole potential; I'm not quite sure if that's what you want or not. It is strongly dependent on the force field.

By default CHARMM assumes a time base, so the stated definition of INTEgrate is wrt. to time starting at zero. For a z profile, you have to change the independent variable to match the z values via EDIT; for a range of -40 to 40 in 0.1 A intervals, something like

edit chg delta 0.1 skip 1 offset -40.

would be needed.

Perhaps you should reconsider writing your own program for this.

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