Re: Lone pair disconnected after minimization

From: David Hardy (
Date: Tue Mar 16 2021 - 17:23:59 CDT

Dear Rabiul,

This sounds suspiciously that NAMD was not actually aware of the lone pairs, i.e., your PSF file might be wrong. First, can you please verify that your PSF file actually has lone pairs properly defined in it (e.g., grep for the NUMLP section of your PSF)? When you list out the NUMLP section of your PSF file, do you see the supporting atom definitions for all of the lone pairs listed in your NATOM section? Finally, near the top of your log file output, do you see LONE PAIRS listed under STRUCTURE SUMMARY? Is it the same number of lone pairs that you defined in your PSF file?

Best regards,

David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801,
> On Mar 15, 2021, at 4:36 AM, Rabiul Gazi <> wrote:
> Dear Experts,
> I am dealing with a chlorobenzene derivative molecules water system. The system contains 10  molecules. After energy minimization it has been observed that lone pairs of chlorine atoms disconnected for few chlorobenzene derivative  molecules.  
> I am using NAMD2.14 for the water system . The psf files were built using psfgen 2.0.
> Please help me in this regard.
> Thank you
>  Rabiul

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