AW: AW: AW: Error in membrane protein simulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Sep 03 2012 - 10:33:31 CDT

Hi,

the long bonds are normal, but you should check with dynmic bonds and low cutoff then to see if the box you set was to small. I can't follow your script now (time), but why don't you use the box you set when solvating??

For better view, but maybe not reliable is to do the wrap with -compound res

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von amin_at_imtech.res.in
> Gesendet: Montag, 3. September 2012 13:27
> An: Norman Geist
> Cc: ajasja.ljubetic_at_gmail.com; namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: AW: namd-l: Error in membrane protein simulation
>
> Thanks. I tried as you said and after pbc wrap all I just see a lot of
> long
> lines crossing each other and everything is cluttered together. I used
> the
> following script to calculate the cell dimensions
>
> set sel [atomselect top all]
> echo [measure center $sel]
> set m [measure minmax $sel] ;foreach {j1 j2} $m {} ;foreach {x2 y2 z2}
> $j2 {}
> ;foreach {x1 y1 z1} $j1 {}
> set x [expr $x2 - $x1]
> set y [expr $y2 - $y1]
> set z [expr $z2 - $z1]
> echo $x $y $z
>
> Can you please tell whats wrong here?
>
> Warm regards.
> Amin.
>
> > Ok, another thing you should try is:
> >
> >
> >
> > 1. Load the systems psf and pdb
> >
> > 2. Set the box dimensions you used in namd with pbc set {x y z}
> >
> > 3. Enter pbc wrap
> >
> > 4. Check if there are overlapping atoms now
> >
> >
> >
> > This will show if your box dimensions in XY are correct, if not, you
> will see a
> > lot close atoms.
> >
> >
> >
> > Mit freundlichen Grüßen
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von
> > Ajasja Ljubetic
> > Gesendet: Montag, 3. September 2012 11:16
> > An: amin_at_imtech.res.in
> > Cc: Norman Geist; namd-l_at_ks.uiuc.edu
> > Betreff: Re: AW: namd-l: Error in membrane protein simulation
> >
> >
> >
> > One thing you can try is setting a very large langevin damping, so
> that the
> > atoms don't explode and them minimize and run and minimize and run.
> Also atoms
> > with unknown positions get set to {0 0 0} so check if you have
> multiple atoms at
> > the origin.
> >
> >
> >
> > Regards,
> >
> > Ajasja
> >
> > Example setting:
> >
> > langevinDamping 100;# or even 1000
> >
> > langevinHydrogen yes
> >
> >
> >
> > minimize 500
> >
> > run 50
> >
> > minimize 250
> >
> > run 50
> >
> > minimize 100
> >
> > run 100
> >
> > #etc ...
> >
> >
> >
> > On 3 September 2012 10:41, <amin_at_imtech.res.in> wrote:
> >
> > Thanks for the reply. Yes 9999999 is VDW. I checked for the
> overlapping atoms
> > and there are no ions within the region of the membrane. However the
> water
> > molecules come very slightly below the P1 atoms of the membrane but
> it seems
> > that they are coming from the spaces between the lipid molecules. Can
> these
> > water atoms be causing the trouble? Can you please tell me what else
> I can look
> > for?
> >
> > Regards.
> > Amin.
> >
> >
> >
> >> Hi,
> >>
> >> as you did unfortunately not mention which of the energies are
> 9999999, I can
> >> only guess.
> >>
> >> So I guess it is the VDW energy. If I guess correct, you have
> overlapping
> >> atoms.
> >> The minimizer will mostly never get rid of such bad initial
> conformations. So
> >> you need to find the bad contacts (maybe using vmd and dynamic bonds
> with a
> >> low
> >> cutoff), or just rebuild the system. As you told you have a
> membrane, could it
> >> be that you have ions beside the membrane? Remember periodicity and
> that these
> >> ions are within the membrane then, as they get wrapped at simulation
> start.
> >>
> >> regards
> >>
> >> Norman Geist.
> >>
> >>
> >>> -----Ursprüngliche Nachricht-----
> >>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >>> Auftrag von amin_at_imtech.res.in
> >>> Gesendet: Samstag, 1. September 2012 08:59
> >>> An: namd-l_at_ks.uiuc.edu
> >>> Betreff: namd-l: Error in membrane protein simulation
> >>>
> >
> >>> Dear all,
> >>> I am trying to simulate a protein embedded in a POPC
> membrane. I
> >>> am
> >>> following the NAMD tutorial on membrane proteins. When I go to the
> >>> first
> >>> equilibration step using constraints mentioned in the step "melting
> of
> >>> membrane" I get "Constraints failure in rattle algorithm" with
> >>> rigidbonds
> >>> all and "Atoms moving too fast" with rigidbonds water. I looked for
> the
> >>> solutions in mailing list and tried 1) decreasing time step to 0.5,
> 2)
> >>> increasing minimization steps from 1000 to 10000, 3) increasing
> >>> pairlistdist to 16, 4) setting margin upto 10, 5) gradually heating
> at
> >>> a
> >>> slow rate. Also I noticed that during minimization I have energies
> >>> 9999999. I have checked the atoms mentioned in the error file
> visually
> >>> and they are distributed throughout the membrane.There are more
> than
> >>> 5000
> >>> of them. I made the membrane using VMD membrane plugin. Can someone
> >>> please tell me where I might be making an error.
> >>>
> >>> Regards.
> >>>
> >>> Amin.
> >>>
> >>>
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> >
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> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक
> अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202

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