AMBER Archive (2008)

Subject: RE: AMBER: stripping water from a restart file

From: CHAMI F. (fatima.chami_at_durham.ac.uk)
Date: Fri Oct 24 2008 - 04:58:58 CDT

 

________________________________

From: owner-amber_at_scripps.edu on behalf of Bill Ross
Sent: Fri 24/10/2008 00:48
To: amber_at_scripps.edu
Subject: RE: AMBER: stripping water from a restart file

> I am trying to run an SMD simulation with 4 residues in vacuum and i =
> got the following message :
> Must have more residues than processors!
>
> and job stopped ...does it mean I cant run this simulation on this =
> system

Allocate fewer processors - one should do.

It does run with two processors but again stopped for a different error this time. I pasted the output file here:
 
 NMR restraints: Bond = 0.996 Angle = 0.000 Torsion = 0.000
===============================================================================
 NSTEP = 9000 TIME(PS) = 9.000 TEMP(K) = 324.18 PRESS = 0.0
 Etot = 126.7326 EKtot = 75.3720 EPtot = 51.3606
 BOND = 22.7783 ANGLE = 45.8167 DIHED = 48.3483
 1-4 NB = 27.7251 1-4 EEL = 83.1635 VDWAALS = -5.5026
 EELEC = -171.6326 EHBOND = 0.0000 RESTRAINT = 0.6639
 EAMBER (non-restraint) = 50.6967
 ------------------------------------------------------------------------------
 NMR restraints: Bond = 0.664 Angle = 0.000 Torsion = 0.000
===============================================================================
 Frac coord min, max: -1.343462511348717E-004 0.834361441303091
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

----------------------------------------------------------------------------------------------------------------------------------

I rerun the same job but using the restart file which was written from the previous run but yet it did not resolve it.

I had no problem running SMD in explicit water using restart files extracted from MD ...but trying to run the same simulation in vacuum seems to be not straightforward at all ...

thanks

Fatima

 

Bill
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