I require to use non bonded interaction of ion in my monomer . This was the
reason for the difference in energetics. Without this non bonded
interaction the energetics are good. I used low temperature equilibration
and with a heating with a time step of 0.0005 ps.
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
Can anyone suggest how should I go about to have a non bonded ioninc
interaction in each monomer group.
Thanks
Kirtana
On Sun, Dec 4, 2011 at 3:42 AM, Yong Duan <duan.ucdavis.edu> wrote:
>
> Interesting. Do you have an explanation on why the energies are so
> different?
>
> Looks like you have a poorly equilibrated system. You may want to try
> short equilibration at low temperature.
>
> What time step did you use? Any other relevant information you can provide?
>
> --
> Yong Duan, Ph.D, Professor
> UC Davis Genome Center and
> Department of Biomedical Engineering
> University of California at Davis
> Davis, CA 95616
> 530-754-7632
>
>
>
>
>
>
> On 12/3/11 4:02 PM, "kirtana S" <skirtana4.gmail.com> wrote:
>
> >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 Sun Dec 04 2011 - 10:30:03 PST
