Dear There,
I am new in amber. I am trying to run constant ph molecular dynamics
simulation in implicit solvent. I am following the tutorial given in amber
website. I have some confusion. At first section 2 during heating of the
system (
http://ambermd.org/tutorials/advanced/tutorial18/files/heat.mdin)
they are putting solvent ph to 7.5. I have not understood why they are
heating the system with solvent ph 7.5. If I want to perform simulation in
constant ph 1 or 2, is it necessary to keep solvent ph 7.5 during the
heating step? Secondly at step 3 at first they do the equilibration at
constant ph 4.5 and then perform simulation at various ph using output of
the simulation run at ph 4.5. In my case, if I want simulation at ph 2
then should I put ph value 2 at all the time?
Thanks in advance.
Best Regards
ABhik
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Received on Thu Mar 11 2021 - 08:30:02 PST
