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

From: Mert Gür (gurmert_at_gmail.com)
Date: Thu May 14 2009 - 05:43:46 CDT

Dear Eric,
I got a little bit confused because this is not mentioned in the tutorial.
According to the tutorial I thought it was only enough to generate the
protein dcd file. Now you are telling me that I also have to generate a
protein psf and pdb file. This means that I have to write a conf file for a
simulation in vacuum am I right? Would that give me the correct protein
energies which fit the one I obtained in windows via namd's namdenergy
visual plugin.
Because in that case I wont have for full-system periodic electrostatics
which means that PME's are not included in my results. Hence the result will
be the same with MDenergy. If I am wrong please feel free to correct me.
But when I use vmd's mdenergy extension in windows I think these are
included.
I have 1500 trajectories so I need to evaluate energies using a script that
is why I am not doing calculations in windows.
I tought that by doing the way I did, it would include PME and periodic BC
and give me the energy of the protein (This is I think what vmd does in
windows)
So actually I could reformulate my problem such that the energies for the
protein I obtained via linux tutorial and windows tutorial are different.
Does anybody have a example ubq-get-energy.conf file (It is not included in
the tutorial files)
Best,
Mert

On Thu, May 14, 2009 at 10:52 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:58 CST