Thanks for the suggestion Prof Duan , I will go ahead with this and I have
a question , why does my system give an error of vlimit exceeded when I
turn on ntc=2 and ntf=2 .
I tried this during the heating up my system to 100K in the first step.
Thanks
Kirtana
On Mon, Dec 5, 2011 at 1:04 AM, Yong Duan <duan.ucdavis.edu> wrote:
> OK, great! We made progress.
>
> Here is what I think you need to do. Continue this simulation, but with a
> few changes. I guess you are using water, either SPC-type of TIP-type.
> Either case, you have to constrain bonds with hydrogens using SHAKE.
>
> So, in mdin, change to
>
> ntc = 2, dt = 0.0005, ntb=2, ntp=1, ntx=7, irest = 1, temp0=50K, iwrap=1,
>
> Do this for 100 ps.
>
> However, now, instead of requesting 8 CPUs, it's probably a good idea to
> run as a single-CPU job. This is because your density is too low.
> Adjustment of volume is likely somewhat "profound" which may cause
> problems in particle distribution. So, use a single-CPU, just to be on the
> safe side. This step is going to be very slow. But, I hope we will be able
> to get your issues resolved soon after this step.
>
> Then, again, let us know what happens and give us the last line of the
> restrt file. We go from there.
>
> Yong Duan
>
>
>
> On 12/4/11 7:27 PM, "kirtana S" <skirtana4.gmail.com> wrote:
>
> >Dear Prof Huan as suggested my run for constant volume has the follwing
> >output file (100ps) and my simulations with the changes suggested by Prof.
> >Ross are still running for constant volume run . With the last line of
> >restrt file of the constant volume equilibration as ,
> >
> >-0.9656320 -0.7234634 1.2387118 -0.0016438 0.3676490 0.5369759
> > -0.0261035 -0.0644101 -0.4033354 -0.0212544 -0.4722374 -1.4779635
> > -0.3125664 0.3052983 0.1990176 -0.2009771 0.1658291 -0.4838171
> > 2.5400989 0.5029373 -0.4271449 0.0691893 -0.9203427 0.1377971
> > -0.1631813 0.2341562 -0.9312167 0.3501815 0.0289519 3.2749102
> > -0.7532019 0.1888475 0.4383601 -0.4962693 0.1705994 -0.3073070
> > 65.5994815 33.0830915 61.0861482 90.0000000 90.0000000 90.0000000
> >
> >I made the changes in the constant volume run for a longer time of 100ps
> >with the
> >NSTEP = 200000 TIME(PS) = 100.500 TEMP(K) = 49.59 PRESS =
> >0.0
> > Etot = -31026.6736 EKtot = 980.9767 EPtot =
> >-32007.6503
> > BOND = 2004.2549 ANGLE = 337.2394 DIHED =
> >95.9672
> > 1-4 NB = 81.7096 1-4 EEL = 1852.3733 VDWAALS =
> >5386.4852
> > EELEC = -41978.5181 EHBOND = 0.0000 RESTRAINT =
> >212.8383
> > EAMBER (non-restraint) = -32220.4886
> > Ewald error estimate: 0.1511E-04
> >
> >--------------------------------------------------------------------------
> >----
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >==========================================================================
> >=====
> > A V E R A G E S O V E R 200000 S T E P S
> >
> > NSTEP = 200000 TIME(PS) = 100.500 TEMP(K) = 51.56 PRESS =
> >0.0
> > Etot = -30828.4002 EKtot = 1020.0117 EPtot =
> >-31848.4118
> > BOND = 1931.5726 ANGLE = 334.5731 DIHED =
> >94.7737
> > 1-4 NB = 80.4599 1-4 EEL = 1854.4828 VDWAALS =
> >5331.8505
> > EELEC = -41691.5156 EHBOND = 0.0000 RESTRAINT =
> >215.3913
> > EAMBER (non-restraint) = -32063.8031
> > Ewald error estimate: 0.6008E-04
> >
> >--------------------------------------------------------------------------
> >----
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> >==========================================================================
> >=====
> > R M S F L U C T U A T I O N S
> >
> > NSTEP = 200000 TIME(PS) = 100.500 TEMP(K) = 5.25 PRESS =
> >0.0
> > Etot = 505.3796 EKtot = 103.9502 EPtot =
> >407.2808
> > BOND = 65.2110 ANGLE = 9.5970 DIHED =
> >4.4219
> > 1-4 NB = 1.2607 1-4 EEL = 2.9849 VDWAALS =
> >108.7707
> > EELEC = 559.7710 EHBOND = 0.0000 RESTRAINT =
> >11.6754
> > EAMBER (non-restraint) = 395.6054
> > Ewald error estimate: 0.4336E-04
> >
> >--------------------------------------------------------------------------
> >----
> >
> > NMR restraints on final step:
> >
> >My constant pressure run doesnt go through with a single step as below and
> >does not generate the restrt file and gives a vlimit exceeded errors ,
> >
> >NSTEP = 0 TIME(PS) = 100.500 TEMP(K) = 40.53 PRESS =
> >-440.2
> > Etot = -31414.9447 EKtot = 801.8739 EPtot =
> >-32216.8186
> > BOND = 2004.4452 ANGLE = 336.9385 DIHED =
> >95.7249
> > 1-4 NB = 81.6625 1-4 EEL = 1852.2805 VDWAALS =
> >5389.6193
> > EELEC = -41977.4896 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> > EKCMT = 275.1504 VIRIAL = 1535.2488 VOLUME =
> >132571.2143
> > Density =
> >0.4605
> > Ewald error estimate: 0.9668E-04
> >
> >--------------------------------------------------------------------------
> >----
> >Dear Prof. Ross , if I understood correctly I make the changes for the no
> >shake ntc=1 ntf=1 (for the warming step and also for equilibration ) with
> >time step dt=0.001 and after heating I used ntx=5 with irest=1 .
> >Also let me know if any suggestions on this.
> >
> >Thanks
> >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
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> >> >> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> > >> >>
> >> >> > >> >_______________________________________________
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> >> >> > >>
> >> >> > >>
> >> >> > >> _______________________________________________
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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
> >> >> ====================================================================
> >> >> Sorry for the multiple e-mail addresses, just use the institute
> >> >>appropriate
> >> >> address.
> >> >> _______________________________________________
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> >> >>
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> >>
> >>
> >>
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> >>
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Received on Sun Dec 04 2011 - 22:30:04 PST
