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

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed May 13 2009 - 15:49:24 CDT

Dear Peter,
I generated 1EJG-prot.dcd (Which contains only the protein coordinates)
using catdcd from my dcd file as it was told in the tutorial.
So according to the tutorial (section 2.5) I should be able to read this
coordinates of protein only, for each frame and then run it for 0 time
steps. Hence I will end up with each frames protein energy.
That should be what tells namd that I want the energy of the protein.
That is what I have understand .I may be mistaken.
I will take a look at the pairinteractions command but there was nothing
mentioned about it in that section.

Best,
Mert.

On Wed, May 13, 2009 at 8:03 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> 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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