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
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Received on Tue Mar 23 2010 - 16:00:02 PDT
