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

From: Mert Gr (gurmert_at_gmail.com)
Date: Thu May 14 2009 - 13:00:57 CDT

Dear Peter,
I have skiped that part, you are right I can use it as a script. Thanks a
lot !
ubq-get-energy.conf is in part 2.1.5 Specific Heat of the tutorial.
I really didn't understand how to properly construct it but my analysis went
over the whole trajectory.
Best
Mert

On Thu, May 14, 2009 at 6:33 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> Hi Mert,
> if you are calculating only the energies from protein-protein
> interactions, it doesn't matter whether the water is there or not. PME
> can be used with or without water, so long as your periodic boundary
> conditions are still properly set up.
>
> Did your analysis run any further than the first frame? It should not
> have, if your dcd and psf didn't have the same number of atoms...
>
> Which part of the tutorial is the ubq-get-energy.conf file supposed to
> come from?
>
> BTW, both namdenergy and mdenergy can easily be used in scripts, which
> may be a more convenient way to do analysis on many trajectories. See
> the namdenergy documentation for a summary of the scripting interface.
> Best,
> Peter
>
> Mert Gür wrote:
> > 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
> > <mailto: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 <mailto: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--000e0cd251521f8ef00469e31c14--

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