This is probably unlikely, but is there a bad overlap near the periodic
boundary? Minimization usually (always?) ignores PBCs. If a molecule is
immediately being wrapped through the wall onto another molecule then
things won't be happy. That could maybe be happening during the second
minimization after the NVT dynamics, which you probably shouldn't need.
Brian
On Sun, Dec 4, 2011 at 1:52 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
> There are many reasons that things like what you observed could happen. If
> you provide us a bit more detail, we might be able to find out why and
> make suggestions.
>
>
>
> Did you turn on the non-bonded interactions of the ion when you minimized
> the structure (before you started the MD simulation)? The differences are
> not limited to non-bonded energy terms. Instead, all energy terms in
> minimization and in MD were really different. For example, bond energy
> more than doubled from 6004.1653 in minimization to 12704.4067 in the
> first step of MD (as indicated by your TIME(PS) = 0.000). Usually, when
> you start a simulation from a structure that was minimized, the energies
> should be reasonably close at the first step. In fact, we would be
> concerned if they are not. If you hadn't told me that they are the same
> system, I would have thought they are completely different systems.
>
> How low was your "low" temperature? Your output says it is 244K. Was this
> close to the your "low" temperature? This temperature is considered low in
> conventional sense, below freezing point of water. However, in terms of
> kinetic energy per atom, 244K is really not much lower than the 300K (only
> about 80%). It sometimes helps to start simulations from 10K, although, in
> this case, I am not sure this would help you much.
>
>
> --
> 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 12/4/11 10:22 AM, "kirtana S" <skirtana4.gmail.com> wrote:
>
> >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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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Sun Dec 04 2011 - 11:30:02 PST
