VMD-L Mailing List

From: Yasser Almeida-Hernandez (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Aug 03 2020 - 11:27:40 CDT

 

Thanks!

I patched VMD with the file and the error disappeared. However, it has
the same behavior as before. When the script is executed this is end of
the output for one molecule:

internal hessian size = 141
Cartesian hessian size = 90
Force constant scaling factor=0.889249 for MP2
Harmonic frequencies: 84 (0 imaginary)
Info) ======================
Info) Please cite TopoTools as:
Info) Axel Kohlmeyer & Josh Vermass, (2019). TopoTools: Release 1.8
Info) https://doi.org/10.5281/zenodo.598373
Info) ======================

Creating namespace ::Optimize::Opt0
Starting 4-dimensional optimization.
Starting optimization with following simplex:
0: 45 109 45 109 --> 0.0
1: 84.41201997194999 109 45 109 --> 0.0
2: 45 109.0 45 109 --> 0.0
3: 45 109 60.16954614788738 109 --> 0.0
4: 45 109 45 109.0 --> 0.0
Optimization converged after 0 steps.
1

..with the same:

Info) Using plugin namdbin for coordinates from file min-bondangles.coor
Info) Finished with coordinate file min-bondangles.coor.
Info) Opened coordinate file namd-temp.pdb for writing.
Info) Finished with coordinate file namd-temp.pdb.
Info) Opened coordinate file namd-temp.dcd for writing.
Info) Finished with coordinate file namd-temp.dcd.
ERROR) Invalid last frame: 1

For the other molecule the optimization involves 1 bond and 3 angles.
The script reaches:

internal hessian size = 208

Cartesian hessian size = 84

Force constant scaling factor=0.889249 for MP2

Harmonic frequencies: 78 (0 imaginary)

.. and stops. I don't know if it is calculating or just stuck. The end
of the debug file is:

D53 dihed {26 9 10 3} -133.5238 {0.3172 4 0.0} Q {}
 D54 dihed {26 9 10 27} 15.5747 {0.4222375 4 195.5747} Q {}
 D55 dihed {7 11 12 13} 92.1424 {6.097440000000001 5 272.1424} Q {}
 D56 dihed {7 11 12 21} -142.1735 {3.5008280000000003 5 180.0} Q {}
 D57 dihed {15 11 12 13} -136.1296 {0.5325 5 43.87039999999999} Q {}
 D58 dihed {15 11 12 21} -10.4454 {0.868048 5 169.5546} Q {}
 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 {}

This is the same behavior I get with version 1.9.3

Any thought?

Yasser

On 03.08.2020 17:31, Gumbart, JC wrote:
> Ah, you found a recently introduced g09 compatibility issue that we
> fixed just a couple of months ago. Please replace your
> fftk_SharedFcns.tcl in the plugins/noarch/tcl/fftk1.3/ directory with
> the one attached and try again.
>
> Best,
> JC
>
>> On Aug 3, 2020, at 10:46 AM, Yasser Almeida-Hernandez
>> <yasser.almeida-hernandez_at_uni-due.de> wrote:
>>
>> Hi JC,
>>
>> I tried one of the 1.9.4 alpha with two molecules. Again, when
>> hitting 'Run optimization' nothing happens except that it writes the
>> TCL script. When the script is executed in the Tk console, it raises
>> an error:
>>
>> Action halted on error!
>> The following QM output file was not recognized:
>>
>> I used Gaussian G09 for the hessian calculation.
>>
>> Any thought?
>>
>> Yasser
>>
>> On 03.08.2020 16:28, JC Gumbart wrote:
>>> Can you try using one of the latest 1.9.4 alpha builds and see if
>> the
>>> problem still occurs?
>>>
>>> Best,
>>> JC
>>>
>>>> On Aug 3, 2020, at 7:46 AM, Yasser Almeida-Hernandez
>>>> <yasser.almeida-hernandez_at_uni-due.de> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I am optimizing 2 angles in a molecule (VMD for LINUXAMD64,
>> version
>>>> 1.9.3). After filling all fields and hit 'Run optimization'
>> nothing
>>>> happens. I generated the TCL script, and when executed, it runs
>>>> apparently OK but the end of the BondedOpt.debug.log ends with:
>>>>
>>>> NAMD run complete
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> DONE
>>>> downhill: optimization -downhill -tol 0.001 -iter 500 -function
>>>> ::ForceFieldToolKit::BondAngleOpt::optBondsAngles
>>>>
>>>> Raw Result: {45 109 45 109} 0.0
>>>>
>>>> DONE
>>>>
>>>> The BondedOpt.log is:
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>>>
>>>> FINAL PARAMETERS
>>>> angle {CG2O5 CG321 OG301} 45.0000 109.0000
>>>> angle {CG2O5 CG321 OG303} 45.0000 109.0000
>>>> END
>>>>
>>>> ... so no angle is optimized, since those are the initial values.
>> I
>>>> set those as initial and repeated but got the ame result.
>>>>
>>>> Also in the VMD terminal it states:
>>>>
>>>> ERROR) Invalid last frame: 1
>>>> Info) Using plugin namdbin for coordinates from file
>>>> min-bondangles.coor
>>>> Info) Finished with coordinate file min-bondangles.coor.
>>>> Info) Opened coordinate file namd-temp.pdb for writing.
>>>> Info) Finished with coordinate file namd-temp.pdb.
>>>> Info) Opened coordinate file namd-temp.dcd for writing.
>>>> Info) Finished with coordinate file namd-temp.dcd.
>>>> ERROR) Invalid last frame: 1
>>>> Info) Using plugin namdbin for coordinates from file
>>>> min-bondangles.coor
>>>> Info) Finished with coordinate file min-bondangles.coor.
>>>> Info) Opened coordinate file namd-temp.pdb for writing.
>>>> Info) Finished with coordinate file namd-temp.pdb.
>>>> Info) Opened coordinate file namd-temp.dcd for writing.
>>>> Info) Finished with coordinate file namd-temp.dcd.
>>>> ERROR) Invalid last frame: 1
>>>> Info) Using plugin namdbin for coordinates from file
>>>> min-bondangles.coor
>>>> Info) Finished with coordinate file min-bondangles.coor.
>>>> Info) Opened coordinate file namd-temp.pdb for writing.
>>>> Info) Finished with coordinate file namd-temp.pdb.
>>>> Info) Opened coordinate file namd-temp.dcd for writing.
>>>> Info) Finished with coordinate file namd-temp.dcd.
>>>> ERROR) Invalid last frame: 1
>>>> Info) Using plugin namdbin for coordinates from file
>>>> min-bondangles.coor
>>>> Info) Finished with coordinate file min-bondangles.coor.
>>>> Info) Opened coordinate file namd-temp.pdb for writing.
>>>> Info) Finished with coordinate file namd-temp.pdb.
>>>> Info) Opened coordinate file namd-temp.dcd for writing.
>>>> Info) Finished with coordinate file namd-temp.dcd.
>>>> ERROR) Invalid last frame: 1
>>>>
>>>> What ERROR) Invalid last frame: 1 means? I read the thread
>>>>
>> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html
>> [1]
>>>> [1] but was not very helpful.
>>>>
>>>> Any help or advice with this issue will be very much appreciated
>>>> since I have been stuck with this since a while.
>>>>
>>>> Best,
>>>> 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
>>>
>>>
>>>
>>> Links:
>>> ------
>>> [1]
>> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html
>> [1]
>
>
>
> Links:
> ------
> [1] https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html