Dear GROMACS users/developers
I've recently started a PhD and am currently looking at bilayer
formation of two-tailed alkyl phosphate esters. I've been using the
PRODRG server to generate topologies for use in GROMACS, and as per the
recommendations made in the paper by Lemkul et. al I have consistently
altered the charges/charge groups according to the charges reported in
similar molecules for which topologies are well established. However,
the "similar molecules" to which I'm referring to are phospholipids such
as DPPC rather than the alkyl phosphate esters in which I'm interested,
and as such I was concerned that the charges [for the alkyl phosphates]
I was implementing might not be entirely accurate. I therefore set about
rather ham-fistedly doing Bader analysis on the individual alkyl
phosphate molecules I'm studying to try to establish more realistic
charges to implement in the topology (more accurately: I ran the same
simulations concurrently with the established molecules like DPPC and
tried to find a relationship between their Bader charges and topologies
which I could use to make a realistic estimate of the charges on the
alkyl phosphate molecules).
I really have two questions and hoped that I might take the opportunity
to ask experienced users/scientists: the first is whether I'm wrong and
that in your opinion(s) it is in fact sensible to simply use the charges
from, say, DPPC in my alkyl phosphate molecules, and the second question
is - regardless of the answer to the first question - whether what I'm
doing is in your opinion(s) sensible. I hope these aren't inappropriate
questions.
Many thanks
--
Ben Ahmady
EngD candidate
M3S Doctoral Training Centre
University College London
Please try to avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
