Hi all,
I've been trying to run some folding simulations of a protein in chloroform
by using aMD. For this I already did an equilibration of the system using
the NpT ensemble (considering that some changes in the volume might occur
as a consequence of the folding). I calculated the parameters as exposed
both in the amber tutorials and in the manual, and after submitting the
job, the potential energy goes incredibly high (usually "*" values). This
is probably because the parameters are used for simulations in water and
not for chloroform, but even using a really small alphaP value gives a
rapid increase in potential energy. Does anyone have any experience with
using aMD and solvents besides water? I'm more or less new to AMBER, so
sorry if the info is elsewhere, but I wasn't able to find anything related
to this.
Best regards,
--
Stephan Schott V.
Bioquímico / Licenciado en Bioquímica
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Received on Tue Jul 19 2016 - 08:30:02 PDT
