VMD-L Mailing List

From: Yasser Almeida-Hernandez (yasser.almeida-hernandez_at_uni-due.de)
Date: Tue Aug 11 2020 - 05:32:05 CDT

Hi JC,

Thanks a lot, it worked!
You are right, I was generating the hessian input file from a different
chk file of a different geometry optimization.

Bests,
Yasser

On 10.08.2020 23:19, JC Gumbart wrote:
> 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
>>