Re: [AMBER] constant pressure

From: Yong Duan <duan.ucdavis.edu>
Date: Sun, 04 Dec 2011 10:52:50 -0800

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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Received on Sun Dec 04 2011 - 11:00:03 PST
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