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
>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Tue Mar 23 2010 - 09:30:03 PDT
