Yes you are right for the steps I followed.
I will run the simulation again. I have a question on use of nsnb (non
bonded interaction updates) , here the default nsnb=25 is used should I
change this .
My simulation has good energetcs for the run without the ion interaction.
Is this alright to have a non bonded ion in the monomer and use solvatebox
in xleap to study the interaction at specific concentration in water.
As suggested I have submitted for 100ps (constant volume) adn we can go
from the results from there.
Thanks for all your time and I appreciate.
Kirtana
On Sun, Dec 4, 2011 at 3:43 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
> Looks like you did following, correct me if I am wrong,
>
> 1) minimization by 100 steps (recorded in min2.dat), final RMS = 3.96
> kcal/mole. Unconstrained, ntb=1.
> 2) From above minimized structure, you started 1000-step MD, as in
> heat1.dat. dt=0.5 fs, ntb=1, ntc=1, residues 1-44 constrained, temp0=50.0.
> You ran this using 8 CPUs.
> 3) You then re-started the simulation from 2) for 1000 steps, again,
> dt=0.5 fs, ntb=1, ntc=1, residues 1-85 constrained, temp0=50.0.
> 4) You then re-started the simulation from 3). You switched to ntb=2,
> dt=1fs. Here, you ran into trouble because the energy changed a lot. At
> the end of 3), VDW=4663 and changed to 132571, indicating you had a couple
> of atoms too close to each other.
>
> It appears that you had ntb=1 or ntb=2 for all of the calculations. So,
> the PBC appears to be ok.
>
> Can you run step 3) for 100 ps? Just run it longer, much longer, with
> exactly the same input files. After that, show us the last line of the
> restart file. We go from there.
>
> --
> 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 11:52 AM, "kirtana S" <skirtana4.gmail.com> wrote:
>
> >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
>
>
>
> _______________________________________________
> 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 - 13:00:04 PST
