VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Wed May 23 2018 - 09:37:49 CDT

Hello,

By default, NAMDEnergy is tailored for CHARMM/AMBER simulations.
However, from what I see, you're trying to do calculations with Martini.

Martini uses different switch/cut-off ranges for Lennard-Jones and
Coulomb interactions, namely, a 9-12 range for Lennard-Jones, and a 0-12
range for Coulomb electrostatics.  The 0-12 coulomb options, by default,
are hardcoded in the martiniSwitching option which, to my understanding,
is not written to the configuration file generated by NAMDEnergy.

Furthermore, martini requires "cosAngles" to be enabled, in order to
properly model angle potentials.

Finally, unless you are using the polarizable water model and a
dielectric constant lower than 15, PME is pretty much useless with Martini.

Any of the three aforementioned reasons could be the cause of your
crash, most likely the lack of 0-12 coulombic switch/cutoff values that
influence electrostatics.  The only reason you didn't see it in your
first calculation is probably the fact that you used a subset of your
system.  In fact, I would suggest that you re-evaluate the results of
the calculation that didn't crash, since they are most likely erroneous.

You can do the following: use NAMDEnergy's '-debug' flag so that you
keep all temporary files produced.  Then, open the configuration file
that was produced (namd-temp.namd) and change all topology/force-field
related options to the ones you used in your simulation
(martiniSwitching on, cosAngles  on, etc).  Make sure that you keep the
following lines:

pairInteraction         on
pairInteractionGroup1 1
pairInteractionFile   namd-temp.pdb
pairInteractionGroup2 2 ;# this is when you want to do calculations with
a second selection, otherwise comment it out
#pairInteractionSelf         on ;#this is for when you want only one
selection, if so, uncomment it and comment out pairInteractionGroup2
coordinates namd-temp.pdb

You can find more about them here:
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node75.html
Briefly, the namd-temp.pdb is your system, but with extra labeling for
the atoms (by default, in their b-factor column) in the selections you
use in your calculations.  (1 for the first selection, 2 for the second
selection)

Then, you can run your calculation using NAMD itself:

namd2 namd-temp.namd > energy.log

The produced log file will just have the reported energy terms for each
timestep.  You can then parse it with a script or NAMD plot and draw
curves or compute averages.

Basically, the above is what NAMDEnergy essentially does: it prepare sa
pdb file with proper b-factor labels for the selection, it writes a
configuration file with the options you set in the GUI/tkConsole and
with pairInteraction terms, it calls namd2 for the calculation and,
finally, it parses the output log and isolates energy terms.

Good luck,
Fotis

On 05/23/2018 04:42 PM, Peter Mawanga wrote:
> Greetings to everyone
>
> I calculated the non-bonded interactions (VdW and Electrostatic)
> between two selections, using the same "cutoff" and "switch" distance
> as employed in simulations:
>
> ============================================================================
>
> namdenergy -vdw -elec -nonb -sel [atomselect top "segname AP1"]
> [atomselect top "segname AP2"] -exe ../namd2 -extsys
> relaxation/equil_out.xsc -T 310 -switch 9 -cutoff 12 -pme -par
> ../martini-protein-bonds.par -par ../martini-protein-angles-cos.par
> -par ../martini-protein-dihedrals.par -par ../martini-all-nonb.par
> -ofile "nonb_pep.dat"
>
> ============================================================================
>
>
> However, when I tried to calculate the interaction energy within the
> system:
>
> ============================================================================
>
> namdenergy  -elec -sel [atomselect top all] -exe ../namd2 -extsys
> relaxation/equil_out.xsc -T 310 -switch 9 -cutoff 12 -pme -par
> ../martini-protein-bonds.par -par ../martini-protein-angles-cos.par
> -par ../martini-protein-dihedrals.par -par ../martini-all-nonb.par
> -ofile "nonb_sys.dat"
>
> ============================================================================
>
>
> I got the following error:
>
> ============================================================================
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Low global exclusion count! (266 vs 268)  System
> unstable or pairlistdist or cutoff too small.
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> Charm++ fatal error:
> FATAL ERROR: Low global exclusion count!  (266 vs 268)  System
> unstable or pairlistdist or cutoff too small.
>
> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>
> ============================================================================
>
> Any insight regarding this error would be highly appreciated.
>
> --
> Cheers
> Peter 

-- 
*******************************************
Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************