Re: [AMBER] constant pressure

From: kirtana S <skirtana4.gmail.com>
Date: Sun, 4 Dec 2011 14:52:54 -0500

When I used low temperature simulation , I have attached the output files
of the minimization and equilibration (I used minimization of solvent
followed by minimizationof entire system , equilibration at 50K at constant
volume and then I turn on constant pressure equilibration) I also tried
skipping my last minimization step still I get difference in the energetics
and error message .

As said "Did you turn on the non-bonded interactions of the ion when you
minimized the structure (before you started the MD simulation)? " , do you
refer to any input file parameter here. Can you tell me which parameter I
should use .I have attached the files if you have any suggestion, I
appreciate your help.

Thanks
Kirtana
On Sun, Dec 4, 2011 at 2:14 PM, Brian Radak <radak004.umn.edu> wrote:

> 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
> > >> >>
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> >_______________________________________________
> > >> >AMBER mailing list
> > >> >AMBER.ambermd.org
> > >> >http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >_______________________________________________
> > >AMBER mailing list
> > >AMBER.ambermd.org
> > >http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ 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
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Sun Dec 04 2011 - 12:00:03 PST
Custom Search