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
>> >> > >> >>
>> >> > >> >>
>> >> > >> >> _______________________________________________
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>> >> > >> >>
>> >> > >> >_______________________________________________
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>> >> > >>
>> >> > >>
>> >> > >> _______________________________________________
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>> >> > >>
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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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Received on Sun Dec 04 2011 - 22:00:03 PST
