From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Fri Oct 27 2006 - 18:01:00 CDT
hi vishal
have you checked your structure (pdb and psf file) from which you
are running your simulation, to see if there is any abnormally long bond
between two atoms? you should check your protein structure visually to
ensure that your structure is right. i was also getting this error then i
checked my structure and found that there is a bond between hydrogen and one
of the carbon of my ligand that was more then 15 A long.
Dhiraj
On 10/27/06, Vishal Kopardé <vnk_sim_at_yahoo.co.uk> wrote:
>
> Even after minimizing for 10000 timesteps of 1fs I keep getting atoms
> moving too fast error. Can anyone suggest how to get around this?
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Atom 4428 velocity is -21402 -27758.4 -9891.47 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> Stack Traceback:
> [0] CmiAbort+0x35 [0x73428d]
> [1] _Z8NAMD_bugPKc+0x8a [0x49a98a]
> [2] _ZN10Controller9integrateEv+0x429 [0x5a9e31]
> [3] _ZN10Controller9algorithmEv+0x560 [0x5a37a0]
> [4] _ZN10Controller9threadRunEPS_+0x14 [0x5b0ab4]
> [5] /usr/global/namd/namd2 [0x6c8955]
> [6] /usr/global/namd/namd2 [0x754aae]
> [7] Charm++ Runtime: Converse thread (qt_args+0xcf [0x754c01])
> Fatal error on PE 0> FATAL ERROR: Bad global exclusion count!
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
>
> Regards,
> Vishal
>
>
> On Oct 27, 2006, at 12:15 PM, JC Gumbart wrote:
>
> > That depends on what you are trying to accomplish.
> >
> > This question can be answered logically by just thinking about it.
> > What do you think the solution is?
> >
> > On Oct 27, 2006, at 3:32 AM, Dhiraj Srivastava wrote:
> >
> >> Hi all
> >> I want to constrain the position of my protein atoms during
> >> equilibration and for that i need to specify the constraint
> >> reference file. should i write the constraint reference file from
> >> the restart.coor file of previous simulation or should it be the
> >> original pdb file from which i am doing my simulation?
> >>
> >> thanks for advice.
> >>
> >> --
> >> Dhiraj Kumar Srivastava
> >> Department of Chemistry
> >> University of Missouri-Columbia
> >> MO, 65211
> >>
> >
>
> Send instant messages to your online friends http://uk.messenger.yahoo.com
>
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:45 CST