I wouldn't vary vlimit. If the vlimit is being reached consistently it
means something went wrong. I would probably attribute it to an imperfect
reimaging. You'll probably have to re-heat your system and re-equilibrate
it rather than using the pre-imaging velocities. Visualizing your system
would definitely help tell you what's going on. Another thing you can do is
take one of your .rst files that's not corrupted and re-run that part of the
calculation with iwrap=1 (i'm assuming amber8 has it, i've never used that
version).
Good luck!
Jason
On Thu, Aug 26, 2010 at 4:25 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Hai,
> I am running TI calculations for my substrate molecule in explicit solvent
> model under periodic conditions using Amber8. While decharging the
> substrate
> at clambda=0.702, the .rst file got corrupted after 19ns of simulations. I
> have reimaged the coordinates using ptraj and made new .rst file by using
> successfully executed previous velocities. Now it is giving the following
> error in the output
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 119211
> | TOTAL SIZE OF NONBOND LIST = 953273
> vlimit exceeded for step 0 ; vmax = 52.8470315993812
> vlimit exceeded for step 1 ; vmax = 22.7460132819140
> vlimit exceeded for step 2 ; vmax = 31.0911464420702
> vlimit exceeded for step 3 ; vmax = 32.0430965729679
> vlimit exceeded for step 4 ; vmax = 22.4283085334279
> vlimit exceeded for step 5 ; vmax = 30.6297351749088
> vlimit exceeded for step 13 ; vmax = 21.1358892160258
> vlimit exceeded for step 14 ; vmax = 23.7006086177260
> vlimit exceeded for step 15 ; vmax = 22.4474391113102
> vlimit exceeded for step 16 ; vmax = 20.7900459924269
> vlimit exceeded for step 17 ; vmax = 20.1032519039889
> vlimit exceeded for step 195 ; vmax = 20.1707663969635
> vlimit exceeded for step 196 ; vmax = 21.4009477638104
> vlimit exceeded for step 197 ; vmax = 20.7909547141524
> vlimit exceeded for step 198 ; vmax = 20.2880610335528
> vlimit exceeded for step 199 ; vmax = 20.1838042173541
> vlimit exceeded for step 200 ; vmax = 20.1165430903398
> vlimit exceeded for step 247 ; vmax = 23.1588955952152
> vlimit exceeded for step 248 ; vmax = 21.3977532826269
> vlimit exceeded for step 249 ; vmax = 20.7644413826353
> vlimit exceeded for step 282 ; vmax = 21.7334157547555
> vlimit exceeded for step 284 ; vmax = 20.8522942359352
> vlimit exceeded for step 286 ; vmax = 21.8487214911635
> vlimit exceeded for step 287 ; vmax = 21.6351346279635
> vlimit exceeded for step 293 ; vmax = 22.0473044973173
> vlimit exceeded for step 342 ; vmax = 20.2768527237204
> vlimit exceeded for step 343 ; vmax = 20.7416483688580
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 6 20 21
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> The following is the input file for the simulation
> neturalize MMB4
> &cntrl
> ntr=0, nstlim = 1000000,
> ntave = 1000, nscm = 10000,
> ntx =7, irest =1, ntpr = 1000, ntb =1,
> dt =0.001, nrespa =2,
> ntt =3, gamma_ln = 1.0, tempi = 300, temp0 = 300,
> ntc = 2, ntf = 2, tol = 0.00001,
> ntwr = 1000, ntwx =1000,
> icfe = 1, clambda = 0.70292, klambda = 6
> /
>
>
> Should I vary the vlaue of vlimit?
>
> Thanks,
> manikanthan
>
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 26 2010 - 19:00:03 PDT
