From: Chathuranga Siriwardhana (ccs0019_at_mix.wvu.edu)
Date: Mon Feb 22 2021 - 17:41:42 CST
Thanks Jeff,
I'm using NAMD 2.14. Earlier I was using 2.13 and got it updated
Thanks
*Chathuranga Siriwardhana*
Justin Legleiter Laboratory
West Virginia University
Department of chemistry
Clark Hall, Room 561
Morgantown, WV 26505
On Mon, Feb 22, 2021 at 6:34 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
> What version of NAMD are you using? Versions earlier than NAMD 2.14 don’t
> support halogen lonepairs.
>
> Jeff
>
>
> On Mon, Feb 22, 2021 at 17:31 Chathuranga Siriwardhana <
> ccs0019_at_mix.wvu.edu> wrote:
>
>> Hi NAMD users,
>> I'm trying to see the interaction of a small molecule with a protein in
>> NAMD. As the simulation starts the following error appears;
>>
>> ERROR: Margin is too small for 1 atoms during timestep 1004.
>> ERROR: Incorrect nonbonded forces and energies may be calculated!
>> ERROR: Atom 37 velocity is -9148.69 -8900.08 8246.01 (limit is 12000,
>> atom 310 of 311 on patch 0 pe 1)
>> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
>> patch 0 pe 1).
>> FATAL ERROR: Exiting prematurely; see error messages above.
>>
>> Atom 37 is a lone pair on Chlorine in the small molecule. Any help is
>> really appreciated.
>>
>> Thanks
>> Chathuranga
>>
>>
>>
>>
>>
>>
>> *Chathuranga Siriwardhana*
>> Justin Legleiter Laboratory
>> West Virginia University
>> Department of chemistry
>> Clark Hall, Room 561
>> Morgantown, WV 26505
>>
> --
>
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