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Error in umbrella sampling
#38364 11/04/21 04:06 PM
Joined: Oct 2019
Posts: 23
V
vht Offline OP
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Dear all,

I have been trying to run a umbrella sampling for a system containing protein and two ligands with charmm 44b1 version. Here is the warning that I got

. ***** LEVEL 1 WARNING FROM *****
***** CUTNB,CTOFNB,CTONNB are not in correct order.
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

I found a similar post that link to this and it seems that I need to change the order of the CUTNB,CTOFNB and CTONNB in the output (which I did but I got the same warning again).Here is what my question is. Since CUTNB,CTOFNB and CTOFNB have the defaults values, do I need to change the values as well and if it is how to do that?

Even though with this warning, dynamics was ran but terminated giving an error as follow


***** LEVEL -2 WARNING FROM *****
***** ENERGY CHANGE TOLERANCE EXCEEDED
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5

ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -2

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 26.44 SECONDS
CPU TIME: 8.71 SECONDS

What could be the reason behind this ?. The input and output files are attached.

Any help is appreciated.


Thanks
VH

Attached Files
umbrella (copy)_out.txt (848.57 KB, 18 downloads)
SHA1: b7dafcfb583423ae51d5473f6d1b14d184228241
umbrella (copy)_inp.txt (2.18 KB, 18 downloads)
SHA1: 26cbdd1572cec1e155b5f0ff34379ceaa954e26b
Re: Error in umbrella sampling
vht #38365 11/04/21 04:32 PM
Joined: Sep 2003
Posts: 8,579
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rmv Offline
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The cutoff warning is harmless, but will go away if you make CTONNB slightly smaller than CTOFNB.

The energy tolerance exceeded error is not harmless and needs to be addressed, and can arise from several sources.

Causes include too many close VDW contacts, inadequate minimization prior to dynamics, or conflicting restraint terms. I did note a large number of atom selections that reported zero atoms selected, indicating there may be some logic flaws.

You will need to investigate these issues in more detail.


Rick Venable
computational chemist


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