Dear All,
I ran minimization of the solvent, minimization of entire system , constant
volume equilibration and again minimization before the constant pressure
equilibration.
The job gets killed after this step with an error as below, is this
something to do with my input prmtop and inpcrd files
vlimit exceeded for step 1; vmax = 486.1523
vlimit exceeded for step 2; vmax = **********
vlimit exceeded for step 3; vmax = **********
vlimit exceeded for step 4; vmax = **********
vlimit exceeded for step 5; vmax = **********
vlimit exceeded for step 6; vmax = **********
vlimit exceeded for step 7; vmax = **********
vlimit exceeded for step 8; vmax = **********
vlimit exceeded for step 9; vmax = **********
vlimit exceeded for step 10; vmax = **********
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
The last step of minimization has
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -1.2257E+05 9.7831E-01 1.2756E+02 C7 551
BOND = 6004.1653 ANGLE = 1318.8747 DIHED =
205.2874
VDWAALS = 16210.2078 EEL = -153314.2089 HBOND =
0.0000
1-4 VDW = 268.8998 1-4 EEL = 6739.7131 RESTRAINT =
0.0000
and equilibration file has
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 244.40 PRESS =
2013.9
Etot = -17407.5244 EKtot = 18506.4151 EPtot =
-35913.9396
BOND = 12704.4067 ANGLE = 1455.1636 DIHED =
0.3601
1-4 NB = 541.0429 1-4 EEL = 6726.3304 VDWAALS =
5828.9860
EELEC = -63170.2293 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 6364.7776 VIRIAL = -20026.3462 VOLUME =
606942.3409
Density =
0.3860
Ewald error estimate: 0.2325E-03
------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 486.1523
vlimit exceeded for step 2; vmax = **********
Thanks for suggestion
Kirtana
On Sat, Dec 3, 2011 at 6:07 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Dec 03, 2011, kirtana S wrote:
> >
> > While running constant pressure equilibration after minimization I get
> the
> > following error
> >
> > vlimit exceeded for step 1; vmax = 365.9801
> > vlimit exceeded for step 2; vmax = **********
>
> You should generally equilibrate at constant volume first, and then turn
> on constant pressure. I note that you density is very low, but maybe that
> is what you expect here ("solvent box of monomers"). If not, check to see
> what is going on.
>
> The fact that such bad things happen on the first two steps may have
> nothing
> to do with constant pressure. Be sure that the potential energy starts at
> the
> same place it had at the end of the minimization.
>
> ....dac
>
>
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Received on Sat Dec 03 2011 - 16:30:03 PST
