Dear Anna,
I think it's better to keep one single force field... I don't know
which ff is better for your simulation, but for example you can
manually correct the definition that PRODRG gives you and adjusting it
for GROMOS 53a6 paramenters.
Valerio
anna.marabo...@isa.cnr.it ha scritto:
Dear all,
I have to perform a simulation in which a protein with a ligand is
included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
membrane simulations, I see that the chosen forcefield is Gromos96 53a6
manually corrected to include the Berger lipids parameters. However, to
create the topology of the ligand, I usually use PRODRG that produces
the topology and parameters using the Gromos96 43a1 forcefield (it
should do, at least...I see that the web server has recently changed and
I don't see the indication of the forcefield used inside...) My
question is: how to deal with the two different forcefields? I see in
the gmx-user list that the use of different forcefields is strongly
discouraged (and I agree with this suggestion) however if I have to
manage such different systems, what can I do? Can I add the Berger
lipids parameters to Gromos96 43a1 and use this corrected forcefield
instead? I did not understand if the Gromos 53a6 ff was chosen in the
tutorial because it is better than 43a1 to manage such systems, or
because it is more compliant than 43a1 with Berger lipids parameters.
Many thanks for suggestions and best regards.
Anna Marabotti
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