Dear Adrian,
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.
>
> Adrian
>
>
>
> On 3/23/10 8:34 AM, nicholus bhattacharjee wrote:
>
>> Dear Adrian,
>> 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.
>>>
>>> Adrian
>>>
>>>
>>>
>>>
>>>
>>> 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)
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Received on Wed Mar 24 2010 - 22:00:03 PDT
