From: Vishal Kopardé (vnk_sim_at_yahoo.co.uk)
Date: Fri Oct 27 2006 - 17:12:23 CDT
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
>>
>
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