VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 18 2010 - 17:56:52 CDT

On Thu, 2010-03-18 at 22:50 +0000, Nuno Sousa Cerqueira wrote:
> Hello,
>
>
> What am trying to do is the following.
> I have developed a small GUI (Tk interface) so that people can easy
> load several scenes from VMD.

you mean like the "viewmaster" plugin?

> Each scene (dynamic or static scenes) is stored in a directory and
> what I do is to play a vmd state. For dynamics and static scenes this
> works fine.
>
> My idea was to do the same thing with the NAMD interactive
> simulations, for instance the alanine example.
>
> The script that the GUI runs is something like this:
>
> exec namd2 NAMD_1/alanin.conf &
> mol new NAMD_1/alanin.psf type psf
> mol addfile NAMD_1/alanin.pdb type pdb
>
> imd connect localhost 2030
>
>
>
> It woks ok in the first time. But when I change it for another scene
> and select this example again It no longer works.

did you first kill the original namd IMD job?
otherwise it will be hogging the port.

cheers,
   axel.

> There are no errors on the output but instead of observing the alanine
> dynamic I just see the molecule jumping between two states.
>
> Sample output:
>
> nfo) Using plugin psf for structure file NAMD_1/alanin.psf
> psfplugin) no cross-terms defined in PSF file.
> Info) Analyzing structure ...
> Info) Atoms: 66
> Info) Bonds: 65
> Info) Angles: 96 Dihedrals: 31 Impropers: 32 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 12
> Info) Waters: 0
> Warning) Unusual bond between residues: 1 (none) and 2 (protein)
> Warning) Unusual bond between residues: 11 (protein) and 12 (none)
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
> 0
> Info) Using plugin pdb for coordinates from file NAMD_1/alanin.pdb
> Charm++: standalone mode (not using charmrun)
> Info) Finished with coordinate file NAMD_1/alanin.pdb.
> 0
> Charm++: scheduler running in netpoll mode.
> Info) Connected to same-endian machine
> Info) Using multithreaded IMD implementation.
> Charm++> cpu topology info is being gathered!
> Charm++> 1 unique compute nodes detected!
> Info: NAMD 2.7b1 for MacOSX-x86
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60100 for multicore-darwin-x86
> Info: Built Mon Mar 23 02:39:30 CDT 2009 by jim on juneau.ks.uiuc.edu
> Info: 1 NAMD 2.7b1 MacOSX-x86 1 macnuno.local nuno
> Info: Running on 1 processors.
> Info: Charm++/Converse parallel runtime startup completed at 0.134066 s
> Info: 598.246 MB of memory in use based on ps
> Info: Changed directory to NAMD_1
> Info: Configuration file is alanin.conf
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 100000
> Info: STEPS PER CYCLE 20
> Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
> Info: LDB PERIOD 4000 steps
> Info: FIRST LDB TIMESTEP 100
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: MAX SELF PARTITIONS 20
> Info: MAX PAIR PARTITIONS 8
> Info: SELF PARTITION ATOMS 154
> Info: SELF2 PARTITION ATOMS 154
> Info: PAIR PARTITION ATOMS 318
> Info: PAIR2 PARTITION ATOMS 637
> Info: MIN ATOMS PER PATCH 100
> Info: INITIAL TEMPERATURE 300
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 0.4
> Info: NO DCD TRAJECTORY OUTPUT
> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME output
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: NO RESTART FILE
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 7
> Info: SWITCHING OFF 8
> Info: PAIRLIST DISTANCE 9
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> Info: PAIRLISTS ENABLED
> Info: MARGIN 1
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 12.5
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 100
> Info: INTERACTIVE MD ACTIVE
> Info: INTERACTIVE MD PORT 2031
> Info: INTERACTIVE MD FREQ 1
> Info: WILL AWAIT INTERACTIVE MD CONNECTION
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 300
> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> Info: USING VERLET I (r-RESPA) MTS SCHEME.
> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> Info: RANDOM NUMBER SEED 1268952576
> Info: USE HYDROGEN BONDS? NO
> Info: COORDINATE PDB alanin.pdb
> Info: STRUCTURE FILE alanin.psf
> Info: PARAMETER file: XPLOR format! (default)
> Info: PARAMETERS alanin.params
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SUMMARY OF PARAMETERS:
> Info: 61 BONDS
> Info: 179 ANGLES
> Info: 38 DIHEDRAL
> Info: 42 IMPROPER
> Info: 0 CROSSTERM
> Info: 21 VDW
> Info: 0 VDW_PAIRS
> Info: TIME FOR READING PSF FILE: 0.00109315
> Info: TIME FOR READING PDB FILE: 0.000276089
> Info:
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 66 ATOMS
> Info: 65 BONDS
> Info: 96 ANGLES
> Info: 31 DIHEDRALS
> Info: 32 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 198 DEGREES OF FREEDOM
> Info: 55 HYDROGEN GROUPS
> Info: TOTAL MASS = 783.886 amu
> Info: TOTAL CHARGE = 8.19564e-08 e
> Info: *****************************
> Info:
> Info: Entering startup at 0.171621 s, 598.246 MB of memory in use
> Info: Startup phase 0 took 0.00666499 s, 598.246 MB of memory in use
> Info: Startup phase 1 took 0.00684404 s, 598.246 MB of memory in use
> Info: Startup phase 2 took 0.00740099 s, 598.246 MB of memory in use
> Info: PATCH GRID IS 1 BY 1 BY 1
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0.382153 0.103801 -0.409218
> Info: LARGEST PATCH (0) HAS 66 ATOMS
> Info: CREATING 12 COMPUTE OBJECTS
> Info: Startup phase 3 took 0.00722408 s, 598.25 MB of memory in use
> Info: Startup phase 4 took 0.00670385 s, 598.266 MB of memory in use
> Info: Startup phase 5 took 0.00961804 s, 598.266 MB of memory in use
> LDB: Measuring processor speeds ... Done.
> Info: Startup phase 6 took 0.00853109 s, 598.266 MB of memory in use
> Info: CREATING 12 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 705 POINTS
> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 7.99609
> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.88002e-15 AT 7.96477
> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 6.77626e-21 AT 7.99609
> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 6.65646e-16 AT 7.96477
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.00974e-28 AT 8.05838
> Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.03763e-15 AT 7.96477
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 3.15544e-30 AT 7.96477
> Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.69576e-16 AT 10.7209
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 3.30872e-24 AT 7.93332
> Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.17076e-15 AT 7.96477
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 8.27181e-25 AT 7.96477
> Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 1.30075e-16 AT 7.96477
> Warning: Interactive MD failed to bind to port 2031.
> Info: Interactive MD listening on port 1032.
> Info: Startup phase 7 took 0.0116479 s, 598.598 MB of memory in use
> Info: Startup phase 8 took 0.0138009 s, 598.848 MB of memory in use
> Info: Finished startup at 0.250057 s, 598.848 MB of memory in use
>
> Info: INTERACTIVE MD AWAITING CONNECTION
> Info) IMD connection ended unexpectedly; connection terminated.
>
>
> Regards, Nuno
>
>
>
>
> On Mar 18, 2010, at 9:54 PM, Axel Kohlmeyer wrote:
>
> > On Thu, 2010-03-18 at 19:18 +0000, Nuno Sousa Cerqueira wrote:
> >> Hello,
> >>
> >> I am having problems running imd under the shell.
> >
> > what shell?
> >
> >> The alanine molecule seems to be jumping only between two conformers,
> >> and not as it should be expected, i.e., following the dynamic
> >> simulation.
> >>
> >> I use the following script:
> >>
> >>
> >> mol new NAMD_1/alanin.pdb type pdb
> >> mol addfile NAMD_1/alanin.psf type psf
> >
> > not that it makes a difference, but these two lines
> > should be the other way around.
> >
> >> mol delrep 0 top
> >> mol representation Lines
> >> mol color ColorID 0
> >> mol selection {all}
> >> mol addrep top
> >> mol drawframes top 0 {now}
> >> mol representation Licorice 0.300000 10.000000 10.000000
> >> mol color Name
> >> mol selection {resid 7 75 539}
> >> mol addrep top
> >> mol drawframes top 1 {now}
> >> mol rename top GLCliq100C1bar.gro
> >> set viewpoints([molinfo top]) {{{1 0 0 -17.6829} {0 1 0 -18.1038}
> >> {0 0
> >> 1 -20.0221} {0 0 0 1}} {{0.293337 0.0118332 -0.955939 0} {-0.241153
> >> 0.968506 -0.0620104 0} {0.925099 0.248718 0.286952 0} {0 0 0 1}}
> >> {{0.0505537 0 0 0} {0 0.0505537 0 0} {0 0 0.0505537 0} {0 0 0 1}} {{1
> >> 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}}
> >> lappend viewplist [molinfo top]
> >> foreach v $viewplist {
> >> molinfo $v set {center_matrix rotate_matrix scale_matrix
> >> global_matrix} $viewpoints($v)
> >> }
> >> unset viewplist
> >> pbc box
> >> axes location off
> >> rock y by 0.01
> >> animate delete beg 0 end 0 0
> >> animate style rock
> >> animate speed 0.8
> >> animate forward
> >
> > why animate here?
> >
> >>
> >> imd connect 0 2030
> >
> > i the machine running NAMD called "0"?
> > i seriously doubt that. RTFM!
> > this should be something like:
> > imd connect my.machine.somewhere.net 2030
> >
> >> In the background i am running : namd2 alanin.conf
> >
> > if it is local, then of course the machine
> > name could be "localhost" or "127.0.0.1"
> >
> > cheers,
> > axel.
> >
> >>
> >> Regards, Nuno
> >>
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> > http://sites.google.com/site/akohlmey/
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.