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.
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Received on Thu Aug 26 2010 - 13:30:03 PDT
