AW: AW: Error in membrane protein simulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Sep 03 2012 - 04:45:25 CDT

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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>
>
>

______________________________________________________________________
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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