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six Trans-Rot vectors-six
#32269 07/15/13 07:57 PM
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prakash Offline OP
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I've received an error in NMA-DIMB method , could you suggest me how to solve this issue?. Detailed output is attached in a file "a.txt". A brief look at the output file has the following error,

NMDIMB: Iteration number = 0
NMDIMB: Dimension of the reduced basis set = 54
NMDIMB: 54 modes are saved in unit 20

***** LEVEL -3 WARNING FROM *****
***** There are less than six Trans-Rot vectors
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5



Here is the input informations:

I have a protein of 23970 atoms and 1480 residues. The system has following details,
Number of segments = 1 Number of residues = 1480
Number of atoms = 23970 Number of groups = 7331
Number of bonds = 24210 Number of angles = 43853
Number of dihedrals = 64185 Number of impropers = 3822
Number of cross-terms = 0
Number of HB acceptors = 2175 Number of HB donors = 2657
Number of NB exclusions = 0 Total charge = 19.00000.

I have the charmm executable with following stack/heap size ,

1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 35b1 August 15, 2008
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.32-279.2.1.el6.x86_64(x86_64)@loca
Created on 7/15/13 at 11:49:52 by user: saravana

Maximum number of ATOMS: 200000, and RESidues: 80000
Current HEAP size: 81520000, and STACK size: 80000000

The commnd that I used for DIMB-nma analysis is ,

bomlev -2

energy

OPEN WRITe FILE UNIT 20 NAME initial1cp.bas
VIBRan NMODes 100
DIMB ITERations 0 PARDim 50 IUNMode 20 BIG
END

!Do the iterative diagonalization, using the precalculated initial
!basis of 53 vectors. 53 converged modes will be written to unit 10:

OPEN READ FILE UNIT 20 NAME initial1cp.bas
OPEN WRITe FILE UNIT 10 NAME modes1cp.mod
VIBRan NMODes 53
DIMB ITERations 100 TOLErance 0.05 PARDim 30 -
IUNMode 10 IUNRead 20 DWIN
END


FLUCT ATOM MODE 1 THRU 13 TEMP 300 SELE ALL END
FLUCT ATOM MODE 1 THRU 13 RMS SELE ALL END
PRINt NORM VECTOR DIPOLE FLUCtuations RMS
FLUCT ATOM MODE 1 THRU 13 RMS 0.2 SELE ALL END
FLUCT ATOM MODE 1 THRU 13 TEMP 300.0 SELE ALL END
PRINt NORM VECTOR DIPOLE FLUCtuations TEMP 300 RMS
PRINt NORM VECTOR DIPOLE FLUCtuations TEMP 300

Attached Files
a.txt (22.11 KB, 336 downloads)
Re: six Trans-Rot vectors-six
prakash #32270 07/16/13 12:43 AM
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tim Offline
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Don't run with bomlev -2 ... it is unnecessary and may mask errors that are pertinent to your problem. In general, it is best practice to run with bomlev 0 with few exceptions.

Is your structure well minimized? If not, the translational and rotational motions will be spread out among multiple modes. I am not too familiar with how DIMB works, but it seems like this might be your problem. Given that you are seeing negative frequencies in your output file (as far as I can tell), this seems like the first thing to try.


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