Re: [AMBER] constant pressure

From: Yong Duan <duan.ucdavis.edu> Date: Sun, 04 Dec 2011 00:42:53 -0800

--
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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