From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Sep 03 2012 - 04:16:11 CDT
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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> ______________________________________________________________________
> 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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