VMD-L Mailing List

From: Yasser Almeida-Hernandez (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Aug 10 2020 - 04:41:58 CDT

Hi all,

I am parametrizing a molecule with VMD 1.9.4a43 and NAMD 2.14b1, and I
am having problems during the bonds/angles optimization. The
optimization targets 1 bond and 3 angles. After loading the hessian
information, VMD gets stuck and nothing happens.

This is the Gaussian file generated by VMD:
'''
%chk=bonds_angles_opt.chk
%nproc=5
%mem=8GB
# MP2/6-31G* Geom=(AllCheck,ModRedundant) Freq NoSymm IOp(7/33=1)
SCF=Tight Guess=Read

B * * K
A * * * K
L * * * K
D * * * * K
B 5 1 A
B 8 1 A
B 3 2 A
B 8 2 A
B 15 2 A
B 5 3 A
B 19 3 A
B 6 4 A
B 11 4 A
B 14 4 A
B 18 5 A
B 7 6 A
B 24 6 A
B 9 7 A
B 25 7 A
B 12 8 A
B 10 9 A
B 26 9 A
B 11 10 A
B 27 10 A
B 28 11 A
B 13 12 A
B 16 12 A
B 14 13 A
B 22 13 A
B 21 14 A
B 17 15 A
B 20 15 A
B 23 15 A
A 3 5 1 A
A 18 5 1 A
A 2 8 1 A
A 12 8 1 A
A 5 3 2 A
A 19 3 2 A
A 12 8 2 A
A 17 15 2 A
A 20 15 2 A
A 23 15 2 A
A 8 2 3 A
A 15 2 3 A
A 18 5 3 A
A 7 6 4 A
A 24 6 4 A
A 10 11 4 A
A 28 11 4 A
A 13 14 4 A
A 21 14 4 A
A 8 1 5 A
A 19 3 5 A
A 11 4 6 A
A 14 4 6 A
A 9 7 6 A
A 25 7 6 A
A 24 6 7 A
A 10 9 7 A
A 26 9 7 A
A 15 2 8 A
A 13 12 8 A
A 16 12 8 A
A 25 7 9 A
A 11 10 9 A
A 27 10 9 A
A 26 9 10 A
A 28 11 10 A
A 14 4 11 A
A 27 10 11 A
A 14 13 12 A
A 22 13 12 A
A 16 12 13 A
A 21 14 13 A
A 22 13 14 A
A 20 15 17 A
A 23 15 17 A
A 23 15 20 A
D 3 5 1 8 A
D 18 5 1 8 A
D 2 8 1 5 A
D 12 8 1 5 A
D 5 3 2 8 A
D 19 3 2 8 A
D 5 3 2 15 A
D 19 3 2 15 A
D 1 8 2 3 A
D 12 8 2 3 A
D 1 8 2 15 A
D 12 8 2 15 A
D 17 15 2 3 A
D 20 15 2 3 A
D 23 15 2 3 A
D 17 15 2 8 A
D 20 15 2 8 A
D 23 15 2 8 A
D 1 5 3 2 A
D 18 5 3 2 A
D 1 5 3 19 A
D 18 5 3 19 A
D 7 6 4 11 A
D 24 6 4 11 A
D 7 6 4 14 A
D 24 6 4 14 A
D 10 11 4 6 A
D 28 11 4 6 A
D 10 11 4 14 A
D 28 11 4 14 A
D 13 14 4 6 A
D 21 14 4 6 A
D 13 14 4 11 A
D 21 14 4 11 A
D 9 7 6 4 A
D 25 7 6 4 A
D 9 7 6 24 A
D 25 7 6 24 A
D 10 9 7 6 A
D 26 9 7 6 A
D 10 9 7 25 A
D 26 9 7 25 A
D 13 12 8 1 A
D 16 12 8 1 A
D 13 12 8 2 A
D 16 12 8 2 A
D 11 10 9 7 A
D 27 10 9 7 A
D 11 10 9 26 A
D 27 10 9 26 A
D 4 11 10 9 A
D 28 11 10 9 A
D 4 11 10 27 A
D 28 11 10 27 A
D 14 13 12 8 A
D 22 13 12 8 A
D 14 13 12 16 A
D 22 13 12 16 A
D 4 14 13 12 A
D 21 14 13 12 A
D 4 14 13 22 A
D 21 14 13 22 A
'''
.. the calculation is done with Gaussian 09.

The end of the debug file is:
'''
   .
   .
   .
   .
   D59 dihed {11 12 13 3} -23.6656 {0.5330125 4 156.3344} Q {}
   D60 dihed {11 12 13 20} 112.4399 {2.9019 4 292.43989999999997} Q {}
   D61 dihed {21 12 13 3} -144.8614 {1.72641875 4 35.1386} Q {}
   D62 dihed {21 12 13 20} -8.756 {4.8210875 4 171.244} Q {}
loading hessian log file...DONE
'''

The final output in the VMD terminal is:
'''
internal hessian size = 208
Cartesian hessian size = 84
Force constant scaling factor=0.889249 for MP2
Harmonic frequencies: 78 (0 imaginary)
'''
.. and it gets stuck.

Please, any help/suggestions will be very much appreciated.

Bests,
Yasser 

-- 
Dr. Yasser Almeida-Hernandez
Postdoctoral Researcher
Computational Biochemistry
T03 R01 D45
Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2, 45117 Essen
Email: yasser.almeida-hernandez_at_uni-due.de
Phone: +49 201 183 2457