Dear Amber users/develops:
I'm trying to run SMD simulations following the manual and SMD tutorials,
but I find two ways to run it in the manual (section 4.5.2 "jar = 1" and
section 4.7.3 "ncsu_smd" in Amber 11 users' Manual ). I'm confused whether
these two sections are the same when running SMD simulation. And I've tried
the two methods. When I use "jar = 1" in section 4.5.2, the simulation
finished well. But when I use "ncsu_smd", I got the following error: ***
NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' ,*someone
suggested to upgrade the compiler to solve this problem.
Can someone tell me if "jar = 1" method could take place of the "ncsu_smd"
method in SMD simulations? Can I use "jar = 1" throughout the simulations
only?
How can I usd Umbrella Sampling and calculate PMF if the ncsu-error can't
be solved? Is there any other methods to use them?
Hope this helps,
Cuiyl
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Received on Wed Jul 18 2012 - 19:30:03 PDT
