Dear all,
Recently, I want to calculate the solvation free energy of s small molecule fixed (rigid body) using pmemd TI simulations in AMBER.
As far as I know,the only way to achieve constraints generally within AMBER is to use the `belly' option (Cartesian coordinates).
Is there any other way to achieve constraints on the solute in pmemd TI simulations?
But, the "belly" option and "TI" option can not be used together, as is prompted in output "TI is incompatible with belly".
I want to know why both of them can not be used together ? Are there any pitfalls here?
If I modify the code of pmemd by only setting the force and velocity of the fixed molecule zero, will the simulations have any other problems?
Looking forward to your reply.
Thanks for your help in advance.
Pengfei
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Pengfei Li
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Received on Thu Apr 27 2017 - 21:30:03 PDT
