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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 12:59 PM, "kirtana S" <skirtana4.gmail.com> wrote:
>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
>> >> > >> >>
>> >> > >> >>
>> >> > >> >> _______________________________________________
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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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Received on Sun Dec 04 2011 - 13:30:03 PST