Dear Jason,
Thanks a lot for your kindly help. Your relpy is very clear. My input file
is probably flawed in some way, but I can't find where the problem is. And
I'm also confused whether "33.0" in the file " the path = (X, 33.0)
path_mode = LINES" is the value of the variable at the beginning of the
run or at the end of the run? This is my input file:
&cntrl
imin=0, irest=1, ntx=7,
ntpr=1000, ntwr=1000, ntwx=1000,
ntr=1, restraint_wt=500, restraintmask=':470',
nstlim=250000, dt=0.002,
ntt=3, gamma_ln=1, temp0=310, tempi=310, tautp=2,
ntp=1, taup=2, pres0=1,
ntc=2, ntf=2, ntb=2, cut=12,
/
ncsu_smd
output_file = 'smd.txt'
output_freq = 1000
variable
type = DISTANCE
i = (7753, 7828)
path = (X, 33.0) path_mode = LINES
harm = (5000.0)
end variable
end ncsu_smd
~
2012/7/19 Jason Swails <jason.swails.gmail.com>
> 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, ´ÞÓ±è´ <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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 19 2012 - 00:30:03 PDT
