Dear amber users,
I´m working on molecular dynamics simulations of heparan sulphate
models, in my case, having 6 negative charges. When calculating the
dipole moment wiht ptraj I include the HS residues + the 6 Na+
neutralizing ions, as the manual advise for the calculation of dipole
moments. When processing the results over 86 ns, I observe the dipole
moment grows up (with fluctuations) till 6300 debyes (at 0 ns it´s
about 80 debyes). Has anyone ever worked on HS simulations and
calculated the dipole moment? Do you think is it possible such a high
value and such increasing behaviour?
Thank you.
*J.C. Munoz
PhD student.
Institute of Chemical Research (Instituto de Investigaciones Quimicas),
Sevilla, Spain.
Carbohydrates Group.*
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Received on Wed May 26 2010 - 01:31:11 PDT
