From: amin_at_imtech.res.in
Date: Mon Sep 03 2012 - 06:27:14 CDT
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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>>
>>
>>
>
>
> ______________________________________________________________________
> 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
>
>
>
>
______________________________________________________________________
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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