Dear Amber Users,
I’ve a couple of questions regarding the output generated after using the density command in cpptraj (Amber14 and AmberTools15).
When analysing the mass density of water along the z-coordinate in solvated lipid bilayer system I obtain a mass density of ~1500 in the regions where water bulk density of 1.0 g/mL (or 1000 kg/m^3) could be expected. Prior to doing this analysis my lipids where of course centered at the origin, as being described in the membrane tutor found on the amber home-pagel.
To do a double check I’ve also plotted the number density of water across the z-dimension and end up with values of ~250 (the number density of water is around 0.0334 molecules/Å^3). Based upon results obtained from these investigations I of course suspect that numbers that I get has different units and need to be recalculated somehow in order to reach the values that I do expect? Perhaps by using the total number of water molecules or xy-area?
Can someone help me to clarify things?
With kind regards, Bjoern
_________________________________________
Björn CG Karlsson, Ph.D., Associate Professor/Docent
Senior Lecturer
Linnæus University
Faculty of Health and Life Sciences (FHL),
Department of Chemistry and Biomedical Sciences
Norra vägen 49, SE-391 82 Kalmar, Sweden
+46 (0)772-28 80 00 Telephone
+46 (0)480-44 67 40 Direct
bjorn.karlsson.lnu.se<mailto:bjorn.karlsson.lnu.se>
Lnu.se
Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden.
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Received on Tue Oct 13 2015 - 11:30:05 PDT
