Re: Need help to generate ubq-get-energy.conf

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 13 2009 - 12:03:55 CDT

Hi Mert,
there doesn't appear to be anything in your config file that *tells*
namd that you want only the energy of the protein; how is it supposed to
know? Have a look at the pairInteractions command...
Best,
Peter

Mert Gür wrote:
> Hi everyone,
> I am a quite new user of Linux. I have performed a number of MD
> simulations. What I am searching for is the energy of only the protein.
> I have read the linux tutorial of namd and also read the corresponding
> e-mails in this list.
> My problem is that the way I have written my get-energy.conf file either
> does not work properly or does not give me the energy of only the protein.
> I came to this conclusion by comparing the energies both with the ones
> I have obtained via vmd's namdenergy plugin (in windows) and via mdenergy
>
> For example in linux I obtained
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> ENERGY: 3039000 126.4302 379.9730 174.6389
> 23.0378 -57317.3079 5216.9948 0.0000
> 0.0000 10013.9117 -41382.3216 301.2902
> -41358.1629 -41358.1629 301.2902 -976.4120
> -943.0767 178158.8790 -976.4120 -943.0767
>
> whereas in windows I have obtained (which is also close to mdenergy's
> result)
>
> Frame Time Bond Angle Dihed
> Impr Elec VdW Conf Nonbond
> Total
> 0 0 +126.308 +405.648 +188.96
> +17.5462 -476.427 -122.028 +738.463 -598.456
>
> I attached my file in case you are interested. I used 1EJG crambin in my
> simulation so the name of the file is correspondingly different.
> Any help or even an example ..-get-energy.conf file would be appreciated.
> Mert
>
>
>
> structure ../common/1EJG_wb.psf
> coordinates ../common/1EJG_wb.pdb
> binCoordinates ../run4/res.coor
> binVelocities ../run4/res.vel
> extendedSystem ../run4/res.xsc
>
>
> set temperature 300
> set outputname 1EJG
> set restartname res
>
>
> firsttimestep 3039000
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen off
>
>
> ## Periodic Boundary Conditions
> cellBasisVector1 57.9 0. 0.
> cellBasisVector2 0. 53.7 0.
> cellBasisVector3 0. 0. 57.3
> cellOrigin 11.2 10.0 6.3
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 60
> PMEGridSizeY 54
> PMEGridSizeZ 60
>
>
>
> # Output
> outputName $outputname
> restartName $restartname
> outputEnergies 500
> outputPressure 500
> restartfreq 500
> dcdfreq 500
> xstFreq 500
>
> # runs 0 time steps for each frame in the dcd
> # opens the dcd file to read the coordinates
> coorfile open dcd 1EJG-prot.dcd
> set i 0
> while { ![coorfile read] } {
> incr i 500
> firsttimestep $i
> run 0
> }
> coorfile close

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