I have some questions about SANDER and PMEMD. I tried to run GB simulation by
SANDER and also tried the TIP3P water simulation by PMEMD. The system
is a 100 residues protein(charge +9) and the water number is ~8000.
The GB/SANDER is
much slower than the TIP3P/PMEMD. It surprised me because I always think that
implicit solvent is much faster than explicit one. Is it due to the different
between PMEMD and SANDER? If it is, is there any way to run the GB simulation
with higher speed?
The other thing is that PMEMD seems not support the ibelly simulation,
which can fix specific part of protein. Is there any way to do it?
Thank you.
Yuming Morris Chen
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Received on Sun Oct 08 2006 - 06:07:08 PDT
