Re: [AMBER] problem with steered MD

From: Dmitri Nilov <nilovdm.gmail.com>
Date: Tue, 30 Mar 2010 10:37:51 +0400

**Hello!
Regarding the quation of harmonic external force F=kx, rk2 is k/2 in
kcal/mol-A^2. The choice of the force constant is rather empirical and it is
http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=PARK2004

Dmitry Nilov,
Lomonosov Moscow State University

On Thu, Mar 25, 2010 at 8:37 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:

> Thank you for the suggestion. It is working. I just have a
> simple query...
> In dist.RST we write
>
> # Change
> &rst iat=901,5, r2=64.340350, rk2=5000., r2a=100.0, /
>
> where r2 and r2a are the initial and final distance between atom nos 901
> and
> 5. What dose rk2 means and what should be its ideal value?
>
> On Wed, Mar 24, 2010 at 4:20 AM, Adrian Roitberg <roitberg.qtp.ufl.edu
> >wrote:
>
> > Dear Nicholus,
> >
> > first, point, YES, you must be equilibrated (or at least relaxed into a
> > good temperature/density, etc).
> >
> > You should start at the exact value the distance has before you start to
> > pull. Anything different that that value will generate bad oscillations.
> >
> >
> >
> >
> > On 3/23/10 8:34 AM, nicholus bhattacharjee wrote:
> >
> >> Thank you for your suggestion. By the way should I
> >> equilibrate my system before doing SMD? Another query after reading your
> >> reply is that if my initial distance is 29 A than should I start from
> 29.5
> >> (greater than that) or 28.5 (less than that)?
> >>
> >> On Tue, Mar 23, 2010 at 7:46 PM, Adrian Roitberg<roitberg.qtp.ufl.edu
> >> >wrote:
> >>
> >> Hi,
> >>> you need to look at the test cases and follow that a bit. We are
> working
> >>> on
> >>> some tutorials, but they are not yet ready.
> >>>
> >>> I would look at your dist_vs_t file, specially the first line.
> >>>
> >>> If your distance at time zero is really 29 A and you start from 29.5,
> the
> >>> initial restraint will be huge. Given that your initial restraint
> energy
> >>> is
> >>> 3334.5521 and your force constant is 5000, you seems to have a distance
> >>> of
> >>> ~0.8 A away from where you should be.
> >>>
> >>> this causes a very fastm strong pull, followed by shake failures.
> >>>
> >>> Try stating your pull at exactly the distance you really have before
> >>> pulling.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On 3/23/10 5:41 AM, nicholus bhattacharjee wrote:
> >>>
> >>> Dear community,
> >>>> I am trying to do a steered MD of a protein
> of
> >>>> 56
> >>>> residue long. The initial distance between CA atom of 1st residue
> (atom
> >>>> no
> >>>> 2) and CA atom of 56th residue (atom no 905) is 29A. My input and
> >>>> dist.RST
> >>>> files are as follows
> >>>>
> >>>>
> >>>> pro.in>
> >>>>
> >>>> Sample pulling input
> >>>> &cntrl
> >>>> nstlim=5000000, cut=99.0, igb=1, saltcon=0.1,
> >>>> ntpr=500, ntwr=500, ntt=1,
> >>>> ntx=1, ntwx=500, ig=256251,
> >>>> ntc=2, ntf=2, tol=0.000001,
> >>>> dt=0.002, ntb=0, tempi=300., temp0=300.,
> >>>> jar=1
> >>>> /
> >>>> &wt type='DUMPFREQ', istep1=1, /
> >>>> &wt type='END', /
> >>>> DISANG=dist.RST
> >>>> DUMPAVE=dist_vs_t
> >>>> LISTIN=POUT
> >>>> LIST=POUT
> >>>>
> >>>> dist.RST>
> >>>>
> >>>> # Change
> >>>> &rst iat=905,2, r2=29.5, rk2=5000., r2a=50.0, /
> >>>>
> >>>>
> >>>> The output is file is giving errors
> >>>>
> >>>>
> >>>> 4. RESULTS
> >>>>
> >>>>
> >>>>
> --------------------------------------------------------------------------------
> >>>>
> >>>>
> >>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 343.74 PRESS
> =
> >>>> 0.0
> >>>> Etot = 3687.1261 EKtot = 778.3610 EPtot =
> >>>> 2908.7651
> >>>> BOND = 12.4186 ANGLE = 207.4832 DIHED =
> >>>> 678.5772
> >>>> 1-4 NB = 802.1944 1-4 EEL = 3296.4852 VDWAALS =
> >>>> 14.2383
> >>>> EELEC = -3938.2112 EGB = -1498.9728 RESTRAINT =
> >>>> 3334.5521
> >>>> EAMBER (non-restraint) = -425.7870
> >>>>
> >>>>
> >>>>
> ------------------------------------------------------------------------------
> >>>>
> >>>> NMR restraints: Bond = 3334.552 Angle = 0.000 Torsion =
> >>>> 0.000
> >>>>
> >>>>
> >>>>
> ===============================================================================
> >>>> vlimit exceeded for step 0; vmax = 302.9507
> >>>>
> >>>> Coordinate resetting (SHAKE) cannot be accomplished,
> >>>> deviation is too large
> >>>> NITER, NIT, LL, I and J are : 0 1 7 1 2
> >>>>
> >>>> Note: This is usually a symptom of some deeper
> >>>> problem with the energetics of the system.
> >>>>
> >>>> I dont know what to do. Please help. By the way is there any tutorial
> >>>> for
> >>>> steered MD for Amber 9.
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>> --
> >>> Dr. Adrian E. Roitberg
> >>> Associate Professor
> >>> Quantum Theory Project
> >>> Department of Chemistry
> >>>
> >>> Senior Editor. Journal of Physical Chemistry
> >>> American Chemical Society
> >>>
> >>> University of Florida PHONE 352 392-6972
> >>> P.O. Box 118435 FAX 352 392-8722
> >>> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>
> >>
> >>
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project
> > Department of Chemistry
> >
> > Senior Editor. Journal of Physical Chemistry
> > American Chemical Society
> >
> > University of Florida PHONE 352 392-6972
> > P.O. Box 118435 FAX 352 392-8722
> > Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 30 2010 - 00:00:03 PDT
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