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Recentering does not fix resids going out of cell
#32387 08/11/13 10:44 PM
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After recentereing, some resids still float out of unit cell.
I tried to recenter only 5 ns at a time but the result is the same.

Code:
stream toppar.str

read psf card name "/export/lustre_1/mallsopp/dpc/sim1/w-dpc-1.psf"
OPEN UNIT 1 READ CARD NAME "/export/lustre_1/mallsopp/dpc/rg/crd/sim1.crd"
 READ COOR UNIT 1 CARD
 CLOSE UNIT 1
 
coor copy comp

crystal free
crystal define cubi 70 70 70 90. 90. 90.
crystal build noper 0 
image byres sele segid DPC end 
update imgfrq 20 cutim 20.0

set i = 100
set j = 100
label beginloop

open unit @i read unform name /export/lustre_1/mallsopp/dpc/dcd/sim1/dyn@i.dcd

incr i by 1
incr j by 1
if @j .lt. 151 then goto beginloop

open write unit 20 file name micelle-tmp-sim1.dcd    ! Write recenered 

merge first 100 nunit 51 output 20 - !nfile 1000 output @wu -
!sele segid DPC .and. (-
! end -
sele segid DPC .or. segid WAT end -
 recenter -
orient norot sele type C212 .and. resid 1 end

close unit 20

end

Re: Recentering does not fix resids going out of cell
swmmr1928 #32388 08/11/13 10:51 PM
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In another thread, someone mentioned a shift z command. I could not find that in documentation.

Maybe some combination of shifts could fix it.
It looks like this:


I found this piece of code
Code:
COOR STATistics SELE desired-atom END
COOR TRANS  ZDIR ?ZAVE  FACT -1.0

Last edited by swmmr1928; 08/12/13 12:29 AM.
Re: Recentering does not fix resids going out of cell
swmmr1928 #32389 08/12/13 01:35 PM
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I see no obvious reason why this does not work; you should probably also add IMAGE BYRES SELE SEGID WAT END, but that should not influence your DPC. Do you get any output indicating that image centering is being done? You could try removing the "ORIENT NOROT", but that too should not be any problem.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Recentering does not fix resids going out of cell
swmmr1928 #32390 08/12/13 01:51 PM
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To be clear, there is an obvious recentering that occurs from this script. However, the micelle still drifts enough for this problem to occur.

Re: Recentering does not fix resids going out of cell
swmmr1928 #32391 08/12/13 02:48 PM
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OK. You can try doing the merge recenter twice, or increasing the cutoff in your crystal build command to get more images included.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Recentering does not fix resids going out of cell
swmmr1928 #32392 08/12/13 04:51 PM
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There can be issues with this if the micelle is no longer intact due to a simulation run with IMAGE BYRES for the centering, esp. for the ORIENT option. Micelle structures are generally too chaotic for an RMS atom based alignment to be very useful.


Rick Venable
computational chemist

Re: Recentering does not fix resids going out of cell
swmmr1928 #32393 08/12/13 05:55 PM
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Recentering does not depend on any RMS based alignment.
The ORIEnt requested in this case was very focused.
I think the problem was that some residues moved further than one neighbor image between saved frames in the trajectory.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Recentering does not fix resids going out of cell
swmmr1928 #32394 08/12/13 06:09 PM
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Right-- I forgot ORIENT uses the same atom selection as RECENTER.

It could be an issue with the position of the selected atom in the reference structure, though, so it still may be worth trying it w/o the ORIENT NOROT keywords.


Rick Venable
computational chemist

Re: Recentering does not fix resids going out of cell
swmmr1928 #32397 08/13/13 01:47 PM
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I tried recentering twice- running the above script on the output of the above script.

I also tried using crystal build cuto 100.

The resulting trajectory was analyzed with the script developed in this thread.

In both cases, the time series is fluctuating too much to represent a micelle that is not breaking apart from parts leaving the unit cell.

Would you like me to post trajectories, input, outputs?

One idea to bypass this problem which I used during other analysis is to work with all the time series and exclude the affected points. I tried "write all" , however this only writes 8 columns so columns 8-16 are in row 2. Is there a way to write all preserving columns?

Thankyou for the assistance
Matt

Last edited by swmmr1928; 08/13/13 01:59 PM.
Re: Recentering does not fix resids going out of cell
swmmr1928 #32398 08/13/13 03:41 PM
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One way to avoid this problem is to use IMAGE BYSEG for the micelle, so that it remains intact throughout the simulation.

Use the LONGline command prior to writing the data files from CORREL to avoid line wrapping to 80 chars.

I'd probably look at time series of the P atom coordinates to see if I could find one that hasn't been image centered at all, and use that as the target for the RECENTER.

Have you tried w/o ORIENT NOROT yet?

I have resolved z drift in some bilayer simulations by using the COM from the unfolded trajectory; however, this requires starting from a point before any lipids have been separated by image centering.


Rick Venable
computational chemist

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