Negative Born radii with v(z) = 2
Posted: Mon Aug 11, 2008 7:48 am
During MC simulations, when using the option "v(z)_mode [1=linear 2=gauss 3=exp] 2" I get the following message in the log.txt file:
Info: negative born radius (too many terms in descreening sum - use cutoff) t = 0 rbinvf = -0.00251 (ATOM: 790 HA 90 VAL) and the calculated Born radius for atoms from residue 90 given in out_born_radii.dat are:
-------------------------
ATOM RB RBINV VOL Q QB
784 CA (VAL 90) 136.3499 0.0073 0.1044 0.1400 0.1400 CT
785 C (VAL 90) 209.9815 0.0048 0.0632 0.5000 0.5000 C
786 HN (VAL 90) 15.5806 0.0642 0.3460 0.3000 0.3000 H
787 CB (VAL 90) 89.5149 0.0112 0.2181 -0.0600 -0.0600 CT
788 CG1 (VAL 90) 293.5739 0.0034 0.0153 -0.1800 -0.1800 CT
789 CG2 (VAL 90) 70.5150 0.0142 0.4241 -0.1800 -0.1800 CT
790 HA (VAL 90) -399.0489 -0.0025 0.0000 0.0600 0.0600 HC
791 HB (VAL 90) 26.0313 0.0384 0.2869 0.0600 0.0600 HC
792 HG1 (VAL 90) 298.8938 0.0033 0.0201 0.0600 0.0600 HC
793 HG2 (VAL 90) 438.5416 0.0023 0.0031 0.0600 0.0600 HC
794 HG3 (VAL 90) 138.4390 0.0072 0.0345 0.0600 0.0600 HC
795 HG4 (VAL 90) 35.3150 0.0283 0.1456 0.0600 0.0600 HC
796 HG5 (VAL 90) 515.6824 0.0019 0.0073 0.0600 0.0600 HC
797 HG6 (VAL 90) 25.3323 0.0395 0.2545 0.0600 0.0600 HC
-------------------------
After many million steps MC generated the residue 90 makes the alpha helix unwinding. If I use the exponential ("v(z)_mode 3") instead of the gaussian function, no 'Info' message is given in the log.txt file (no negative Born radii) and the helix seems stable.
Info: negative born radius (too many terms in descreening sum - use cutoff) t = 0 rbinvf = -0.00251 (ATOM: 790 HA 90 VAL) and the calculated Born radius for atoms from residue 90 given in out_born_radii.dat are:
-------------------------
ATOM RB RBINV VOL Q QB
784 CA (VAL 90) 136.3499 0.0073 0.1044 0.1400 0.1400 CT
785 C (VAL 90) 209.9815 0.0048 0.0632 0.5000 0.5000 C
786 HN (VAL 90) 15.5806 0.0642 0.3460 0.3000 0.3000 H
787 CB (VAL 90) 89.5149 0.0112 0.2181 -0.0600 -0.0600 CT
788 CG1 (VAL 90) 293.5739 0.0034 0.0153 -0.1800 -0.1800 CT
789 CG2 (VAL 90) 70.5150 0.0142 0.4241 -0.1800 -0.1800 CT
790 HA (VAL 90) -399.0489 -0.0025 0.0000 0.0600 0.0600 HC
791 HB (VAL 90) 26.0313 0.0384 0.2869 0.0600 0.0600 HC
792 HG1 (VAL 90) 298.8938 0.0033 0.0201 0.0600 0.0600 HC
793 HG2 (VAL 90) 438.5416 0.0023 0.0031 0.0600 0.0600 HC
794 HG3 (VAL 90) 138.4390 0.0072 0.0345 0.0600 0.0600 HC
795 HG4 (VAL 90) 35.3150 0.0283 0.1456 0.0600 0.0600 HC
796 HG5 (VAL 90) 515.6824 0.0019 0.0073 0.0600 0.0600 HC
797 HG6 (VAL 90) 25.3323 0.0395 0.2545 0.0600 0.0600 HC
-------------------------
After many million steps MC generated the residue 90 makes the alpha helix unwinding. If I use the exponential ("v(z)_mode 3") instead of the gaussian function, no 'Info' message is given in the log.txt file (no negative Born radii) and the helix seems stable.