VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Aug 10 2020 - 16:19:18 CDT

Hi Yasser,

I finally had a chance to look at the files you sent me. The atom order is different in your PSF/PDB from that in the Hessian log. I guess you changed something about how you built it in the middle of the QM runs. FFTK assumes a 1-1 mapping of atoms between the various files it reads.

Best,
JC

> On Aug 10, 2020, at 5:41 AM, Yasser Almeida-Hernandez <yasser.almeida-hernandez_at_uni-due.de> wrote:
>
> 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
>