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ENERGY CHANGE TOLERANCE EXCEEDED error in the charmm
#37743 11/28/19 12:36 AM
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vht Offline OP
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Hi all,

My system contains a protein with two ligands which was simulated upto 10ns but charmm was aborted with the follwoing error

ENERGY CHANGE TOLERANCE EXCEEDED

Required output file will be attached.

9477 is the starting atom of the ligand in this complex and RTF file generated for this ligand by the charmm-gui.I did not have any crashing problems when running minimization and equilibration prior to simulation.
Is there anyway that I can fix this?.

Thanks
VH

Attached Files
Md-equil.txt (686.54 KB, 56 downloads)
Last edited by vht; 11/28/19 12:48 PM.
Re: ENERGY CHANGE TOLERANCE EXCEEDED error in the charmm
vht #37744 11/28/19 09:51 PM
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The error message
NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 16.39 Angstroms and starts with atom: 9477
Please check group boundary definitions.

is actually very significant (and should probably be assigned a more serious error level). I means that atoms may be missed when the nonbond list is generated, so at the next update there may be surprises. While increasing ECHECK may HIDE the problemis unlikely to solve it.

Probably, somewhere in the deluge of RTFs that you read there is a residue, which you use in your PSF, with inappropriate GROUP delineations. A GROUP should be small (spatial extent less than 12A per the error message).

It is also a good idea to post a complete AND as brief an input file as possible that exhibits the problem (ie, no unnecessary garbage like using CHARMM variables, doing a number of elaborate manipulations - just find the smallest set of commands and the smallest system that shows the problem)

I strongly suggest to read only the RTF/PARAM files that you actually are going to use; if reading everything all the time were optimal, there would be no great need to have several files ...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: ENERGY CHANGE TOLERANCE EXCEEDED error in the charmm
vht #37746 11/29/19 08:22 AM
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Thank you for the reply.

This is the part of the input that use to setup non bonded parameters.

! set up nonbond parameters -- same as for heating
nbond inbfrq -1 imgfrq -1 atom vatom cdie eps 1.0 -
elec ewald pmew fftx 48 ffty 48 fftz 48 kappa .34 spline order 6 -
vdw vswitch cutnb 16.0 cutim 16.0 ctofnb 12. ctonnb 10. wmin 1.0

! We're going to use the Langevin piston method, so we're going to need to
! calculate masses for the pressure and temperature pistons (pmass & tmass)
! calc pmass = total molecular mass / 50
! calc tmass = pmass * 10
scalar mass stat
calc pmass = int ( ?stot / 50.0 )
calc tmass = @pmass * 10

I hope nothing is wrong in these commands


This group contains 89 atoms so it is a larger molecule.The respective rtf for the ligand was generated by chramm-gui.

So as a solution we need to introduce group definitions in RESI definition in RTF of the ligand in order to overcome this problem
I suppose. Is that correct?

I would appreciate if you can give me a guidance to introduce group definitions Since I am beginner to charmm.

Thanks
VH

Re: ENERGY CHANGE TOLERANCE EXCEEDED error in the charmm
vht #37747 11/29/19 09:40 AM
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I just tried to add group definitions to RTF which attached in this post.Don't know whether it is the way. If it is not please let me know the correct way.



Thanks
VH

Attached Files
fad.txt (5.37 KB, 35 downloads)
Last edited by vht; 11/29/19 09:58 AM.
Re: ENERGY CHANGE TOLERANCE EXCEEDED error in the charmm
vht #37748 11/29/19 10:22 AM
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The atoms in each group should be spatially close.
You have to regenerate the PSF with the new RTF.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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