On Wed, Jul 18, 2012 at 10:37 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
Ugh. Correction, the pulling force is *not* constant. The rate at which
the target value for the reaction coordinate changes is constant, there is
a difference.
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
>
--
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 - 20:00:03 PDT
