The nmropt/jar restraints can be easily used to perform umbrella sampling
and steered MD, respectively, and they are drop-in replacements for the
NCSU codes as far as the functionality overlaps.
Note, however, that NCSU codes are far more flexible when it comes to
defining particular restraints -- for instance, jar=1 requires linear
interpolation between the two end-points (that is, the pulling force is
constant). If I recall correctly, NCSU steered MD allows non-linear
traversal of the reaction coordinate. You can also define more flexible
linear combinations of restraints to define reaction coordinates (although
you can generate a LCOD with up to 4 distances in sander using the
nmropt/jar options).
In Amber 11, I think that the NCSU code fails with gcc 4.1.2 (the GCC
version shipped with RHEL 5 and correspondingly CentOS 5), but with later
compilers it should be fine. Are the NCSU tests failing? If not, your
input file is probably flawed in some way.
HTH,
Jason
On Wed, Jul 18, 2012 at 10:11 PM, 崔颖璐 <cuiyinglukitty.gmail.com> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 18 2012 - 20:00:02 PDT
