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

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu May 14 2009 - 02:52:20 CDT

As Peter stated, you will have to generate a separate psf file without
waters as input for the new energy calculations when you reprocess the
dcd through namd.

-Eric

On May 14, 2009, at 2:01 AM, Mert Gür wrote:

> Dear Peter,
> As you can see below (for the first frame ) bond-angle-dihedrals and
> impropers are relatively close values. But when I compare the
> electrical and vdw energies I see that they are at least one order
> different.
> But they seem to be close to the energy of the whole system.
> The only explanation I can think of is that my script includes the
> positions of the water molecules (In its coordinates at the
> beginning ) to all frames
>
> My 1EJG-prot.dcd can't include water molecules cause it is only 10mb
> whereas 1EJG.dcd is 100mb.
> Therefore I am guessing that I am doing something wrong in the script.
>
> Best,
> Mert
>
>
>
> 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
>
>
> On Wed, May 13, 2009 at 11:55 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> > wrote:
> Hi Mert,
> I see... I was confused by the fact that your psf file was named
> "1EJG_wb.psf", which seemed to indicate that it included the water
> box.
> How different are your energies from those of namdenergy/mdenergy?
> Best,
> Peter
>
> Mert Gür wrote:
> > 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
> > <mailto: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
> >
> >
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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