Re: "FATAL ERROR: Bad global improper count" revisited

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Tue Mar 22 2011 - 12:41:42 CDT

Hi Markus,

Things became a little clearer once I had a look at your files that
you sent me. It seems that you have defined 2 improper angles between
your ligand and your protein in the psf file which shouldn't be there.
Check to see how you created your protein system. I removed the
offending angles in the psf file (the 2nd and 3rd improper) and the
calculation continued without problems.

Cheers,
Johan

On Tue, Mar 22, 2011 at 10:42 AM, Markus K. Dahlgren
<markus.dahlgren_at_yale.edu> wrote:
> I have been running equilibration of a single-chain protein complexed with one
> ligand in a 14 Angstrom TIP3P box with PME boundary conditions. I use a 10A
> cutoff and 8A switchdist. After 4ns, using 1fs timestep, I get this error and
> cannot get around it by restarting.
>
> I figure this error has to do with the boundary conditions used. I tried putting
> in the option "splitPatch position" and using the last restart files, but it
> keeps crashing at exactly the same timestep. I have also tried to remove the
> wrapWater and wrapAll options but it does not help. What can I do to get around
> this problem? Should I restart the simualtion from scratch using a different
> cutoff distance, swtichdist, and solvent box size? Would disabling the wrapAll
> and wrapWater options from start help? I have pasted my config file below:
>
>
>
> set name        14A_box
> set outputname      ${name}_equil
>
> set cbv1        77.937         ;# Box size in X dimension
> set cbv2        90.367         ;# Box size in Y dimension
> set cbv3        83.088         ;# Box size in Z dimension
> set cox         -2.118         ;# X coordinate for cell origin
> set coy          1.681         ;# Y coordinate for cell origin
> set coz         -5.830         ;# Z coordinate for cell origin
>
> coordinates     ionized.pdb
> structure       ionized.psf
> if {1} {
> bincoordinates  14A_box_equil.restart.coor
> binvelocities   14A_box_equil.restart.vel
> extendedSystem  14A_box_equil.restart.xsc
> }
> firsttimestep   4034000
>
> rigidBonds      none
>
> set T           310
>
> set outputfreq  100
> set dcdfreq     1000
>
> paraTypeCharmm  on
> parameters      /home/markus/MD_sim/common/opls_MD_mar_18_2011.prm
>
> exclude         scaled1-4
> 1-4scaling      1.0
> switching       on
> cutoff          10
> switchdist      8
> pairlistdist    14
>
> #temperature             $T
>
> langevin                on
> langevinDamping         0.5
> langevinTemp            $T
> langevinHydrogen        no
>
> useGroupPressure        no
> useFlexibleCell         no
> useConstantArea         no
>
> langevinPiston          on
> langevinPistonTarget    1.01325
> langevinPistonPeriod    100
> langevinPistonDecay     50
> langevinPistonTemp      $T
>
> cellBasisVector1        $cbv1   0.      0.
> cellBasisVector2        0.      $cbv2   0.
> cellBasisVector3        0.      0.      $cbv3
> cellOrigin              $cox    $coy    $coz
>
> wrapWater       on
> wrapAll         on
>
> PME             yes
> PMEGridSpacing  1.0
>
> stepspercycle           10
> nonbondedFreq           1
> fullElectFrequency      2
>
> outputname              $outputname
> outputEnergies          $outputfreq
> outputPressure          $outputfreq
> outputTiming            $dcdfreq
> binaryoutput            no
> DCDfile                 $outputname.dcd
> DCDfreq                 $dcdfreq
> DCDUnitCell             yes
> binaryrestart           yes
> restartname             $outputname.restart
> restartfreq             $dcdfreq
> XSTfile                 $outputname.xst
> XSTfreq                 $dcdfreq
>
> timestep                1.0
> run                     20000000
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:58 CST