From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Mon Feb 22 2021 - 18:49:25 CST
Hi Chathuranga,
No worries. I am replying back to the list because I don’t know the answer to your question.
Can anyone on list recommend how to correctly create a PSF with lone pairs?
Thanks,
Dave
> On Feb 22, 2021, at 6:43 PM, Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu> wrote:
>
> Hi David,
> Thank you so much for helping me with my issue. And I am really sorry that I replied to the wrong email. I subscribed to the mailing list today and I got confused with how it works :(
> Would you mind recommending a method to create the psf with lone pairs. I used VMD psfgen.
>
> Thanks again for helping me
>
> Chathuranga
>
>
>
>
>
>
> Chathuranga Siriwardhana
> Justin Legleiter Laboratory
> West Virginia University
> Department of chemistry
> Clark Hall, Room 561
> Morgantown, WV 26505
>
>
> On Mon, Feb 22, 2021 at 7:26 PM David Hardy <dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>> wrote:
> Hi Chathuranga,
>
> It looks to me like NAMD is not treating your atom 37 as a lone pair. The forces on lone pairs are distributed to their support atoms and then set to zero, so I would expect lone pairs to have zero velocity (but I’m having trouble finding that in the code).
>
> If you would post the top of your log file showing the configuration of your system before simulation begins, we could see whether or not your simulation has any lone pairs enabled.
>
> Thanks,
> Dave
>
> --
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>, http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/>
>
>> On Feb 22, 2021, at 5:41 PM, Chathuranga Siriwardhana <ccs0019_at_mix.wvu.edu <mailto:ccs0019_at_mix.wvu.edu>> wrote:
>>
>> 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 <mailto: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 <mailto: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
>> --
>>
>> –––––––––––––––––––––––––––––––––––———————
>> Jeffrey Comer, PhD
>> Associate Professor
>> Department of Anatomy and Physiology
>> Kansas State University
>> Office: P-213 Mosier Hall
>> Phone: 785-532-6311
>> Website: http://jeffcomer.us <https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!oy19tN7QUSKcotZH8b_xfG1SoCSjFRxtAfeYKD73jGbd_OG5PSXl7j1cR8LcY4lt7w$>
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