VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 17 2018 - 09:42:20 CST

Nicolas,
  Thanks for the followup. I sent a note to the NAMD team to see if we
can get that addressed in the next version of NAMD so that this is no
longer a concern going forward.

Best regards,
  John Stone

On Sun, Dec 16, 2018 at 04:38:09PM -0300, Nicolás Veiga wrote:
> Thank you both for the replies.
>
> I have just solved the issue. The problem was that I was using the CUDA
> version of NAMD, which does not support the pair interaction calculation.
> When I changed to NAMD_2.13_Win64-multicore version everything worked
> perfectly.
>
> Regards,
>
> Nicolás.
>
> Dr. Nicolás Veiga
> Profesor Adjunto de QuĂmica Inorgánica
> Facultad de QuĂmica - UdelaR
> Montevideo, Uruguay
> Contacto: +598 924 97 39
>
> From: Mayne, Christopher G
> Sent: Sunday, December 16, 2018 3:53 PM
> To: Gumbart, JC
> Cc: Nicolás Veiga ; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: fftk problem in opt. bonded step
>
> I concur with JC that this is most likely an error that is occurring with
> NAMD. The error traces back to the namdenergy call, specifically;
> however, the traceback doesnâ**t give us enough information to debug the
> problem directly.
>
> Recreating the actual call isnâ**t obvious from the traceback, so I dug
> back into the code.
>
> Load the charge-optimized PSF
> Add the geometry-optimized PDB
>
> set sel [atomselect top all]
>
> namdEnergy::namdenergy -psf <path_to_psf> -exe C:/NAMD/namd2.exe -all -sel
> $sel -cutoff 1000 -par <path_to_parameters>
>
> Note: that a separate â**-par <path_to_parameters>â** will need to be
> added for every required parameter file, including the in-progress files,
> i.e., -par parfile1.prm -par parfile2.prm â*¦
>
> Regards,
> Chris
>
>
>
> On Dec 14, 2018, at 4:04 PM, Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
> Unfortunately thereâ**s no way to know for sure what went wrong. Try
> running something else that uses NAMD, like namdenergy, and see if that
> works. You could also try calling NAMD from the VMD console using exec,
> just as done in the command in the error.
>
> Best,
> JC
>
> On Dec 14, 2018, at 6:38 PM, Nicolás Veiga <nveiga_at_fq.edu.uy> wrote:
>
> Thanks for the prompt reply!
>
> The only new file in my working directory is
> â**BondedOpt.debug.logâ**. It seems that everything went well there.
> The last lines of the file (which is attached to this email) are:
>
> END
>
>
> NAMD run complete
>
> Apart from that, in the VMD working directory I could find the file
> â**min-bondangles.confâ** (which is also attached to this email).
> There is no .log file in this directory.
>
> Regards,
>
> Nicolás.
>
> Dr. Nicolás Veiga
> Profesor Adjunto de QuĂmica Inorgánica
> Facultad de QuĂmica - UdelaR
> Montevideo, Uruguay
> Contacto: +598 924 97 39
>
> From: Gumbart, JC
> Sent: Friday, December 14, 2018 7:51 PM
> To: Nicolás Veiga
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: fftk problem in opt. bonded step
>
> It sounds like something is going wrong with NAMD. Can you happen to
> find that *.namd and *.log file in your directory and see what error
> is there, if any?
>
> Best,
> JC
>
> On Dec 14, 2018, at 3:57 PM, Nicolás Veiga <nveiga_at_fq.edu.uy>
> wrote:
>
> Hello,
>
> I am trying to parameterize a substrate using the force field
> toolkit (ffTK) plugin for VMD. Everything went well until I reached
> the bond and angle optimization step. After the calculation of the
> Hessian matrix, I uploaded the information with the â**Guessâ**
> button. However, when I tried to optimize the parameters, I got the
> following error:
>
> child killed: unknown signal
> child killed: unknown signal
> while executing
> "exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
> (procedure "namdrun" line 56)
> invoked from within
> "namdrun"
> (procedure "namdmain" line 76)
> invoked from within
> "namdmain"
> (procedure "::namdEnergy::namdenergy" line 176)
> invoked from within
> "::namdEnergy::namdenergy -silent -psf
> C:/work/Cu_ala_phe_phen_autopsf_opt.psf -exe C:/NAMD/namd2.exe -all
> -sel atomselect496430 -cutoff 1000 -par C:/w..."
> ("eval" body line 1)
> invoked from within
> "eval ::namdEnergy::namdenergy $args"
> (procedure "namdenergy" line 1)
> invoked from within
> "namdenergy -silent -psf C:/work/Cu_ala_phe_phen_autopsf_opt.psf
> -exe C:/NAMD/namd2.exe -all -sel $sel -cutoff 1000 -par
> C:/work/Cu_ala_phe_phen_initia..."
> ("eval" body line 1)
> invoked from within
> "eval $namdEn"
> (procedure "::ForceFieldToolKit::BondAngleOpt::computePESmm"
> line 39)
> invoked from within
> "::ForceFieldToolKit::BondAngleOpt::computePESmm $moleculeID
> $baIndList $namdEnCommand"
> (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles"
> line 84)
> invoked from within
> "$function $p0list"
> (procedure "construct_initial_simplex" line 22)
> invoked from within
> "construct_initial_simplex [lindex $args 0] $scale"
> (procedure "::Optimize::Opt0::handle" line 91)
> invoked from within
> "$opt initsimplex $baInitial $scale"
> (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line
> 324)
> invoked from within
> "::ForceFieldToolKit::BondAngleOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
> invoked from within
> "::ForceFieldToolKit::gui::baoptRunOpt "
> invoked from within
> ".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
> invoked from within
> ".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} {
> .fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed;
> .fftk_gui.hlf.nb.bondangleopt...."
> (command bound to event)
>
> I have tried to solve the problem by following the instructions in
> [1]https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24850.html
> and
> [2]https://guido.vonrudorff.de/2013/force-field-toolkit-empty-string-during-bonded-optimization/.
> However, I still get the same error message.
>
> Is there a solution for this problem?
>
> Thanks in advance, regards,
>
> Nicolás.
>
> Dr. Nicolás Veiga
> Profesor Adjunto de QuĂmica Inorgánica
> Facultad de QuĂmica - UdelaR
> Montevideo, Uruguay
> Contacto: +598 924 97 39
>
>
> <BondedOpt.debug.log><min-bondangles.conf>
>
>
>
>
>
> References
>
> Visible links
> 1. https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24850.html
> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24850.html
> 2. https://guido.vonrudorff.de/2013/force-field-toolkit-empty-string-during-bonded-optimization/
> https://urldefense.proofpoint.com/v2/url?u=https-3A__guido.vonrudorff.de_2013_force-2Dfield-2Dtoolkit-2Dempty-2Dstring-2Dduring-2Dbonded-2Doptimization_&d=DwMGaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=Mblz2a9PcdFhxI8Na3DESM3xrrwqHupWuf_YM9Jaju4&s=0Sy-jFPNTv7k6igibn5GBpJIwd-TNonN2LXqXv3OPyI&e= 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/