Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run

From: Mamta Mohan (mamta_mohan_at_comcast.net)
Date: Mon Nov 10 2008 - 13:39:18 CST

Dear Peter,

Perhaps I missed some explanation in the previous mail.

The periodic cell I defined I used minmax and listed the coordinates (I can
list the macro if you want). The coordinates of the box are not touched once
box was built. The box itself seems to have shifted after minimization. In
the snapshot I redraw to box to explain my point.

Minimization and production ran as one step (please take a look at config
file)

The snapshots I took by superimposing the two molecules (as explained below
in the mail) to make my point. First molecule is before minimization and
production run, that is psf+pdb and second is after simulation finished
psf+dcd.

>From what I see, water box shifted and protein seems to be drifting
constantly towards the top of the box during production run.

I also think (and please explain me why if I am incorrect) that I do not
have to wrap proteins and ions, I think wrap water should be OK. I can wrap
dcd later for protein and ions.

Thank you.
Mamta Mohan

----- Original Message -----
From: "Peter Freddolino" <petefred_at_ks.uiuc.edu>
To: "Mamta Mohan" <mamta_mohan_at_comcast.net>
Cc: <namd-l_at_ks.uiuc.edu>; <jim_at_ks.uiuc.edu>
Sent: Monday, November 10, 2008 12:26 PM
Subject: Re: namd-l: Simulation issues: water box deformation after
minimization and shifting protein coordinates during production run

> Hi Mamta,
> it is not clear to me why you're surprised by what is happening. You've
> defined a periodic cell that is not centered on the center of your
> system, and told namd to wrap the coordinates of waters, but not
> proteins or ions, that are outside of that cell. After minimization, the
> water box's center is duly shifted. What is the problem?
> Also, why are you defining a completely new periodic cell after
> minimization? Just using the system minmax is meaningless at this point
> because you've wrapped the water but not the protein/ions, so you're now
> telling namd that you have a periodic cell that is made up largely of
> empty space.
> Peter
>
> Mamta Mohan wrote:
>> Dear NAMD team,
>>
>> I am following up a mail I posted before.
>>
>> I would appreciate a response.
>>
>> Thank you.
>> Mamta Mohan
>> ----- Original Message -----
>> *From:* Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *To:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
>> *Cc:* ; Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *Sent:* Wednesday, November 05, 2008 5:59 PM
>> *Subject:* Fw: NAMD mail bounce problem.
>>
>>
>> ----- Original Message -----
>> *From:* Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *To:* jim_at_ks.uiuc.edu <mailto:jim_at_ks.uiuc.edu>
>> *Cc:* Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *Sent:* Monday, November 03, 2008 1:35 PM
>> *Subject:* Fw: NAMD mail bounce problem.
>>
>> Dear Jim,
>>
>> Please find the URL listed below where I have uploaded the files.
>>
>> https://myfiles.neu.edu/xythoswfs/webui/_xy-5085581_1-t_uX8Syp73
>> Here you will find zipped files which you can download. file names to
>> be downloaded are listed below.
>> 1STN_lbl_ionized_sim3_configuration_file
>> 1STN_lbl_ionized_water_box_and_protein_PDB_PSF
>> ionized_sim_run3 - dcd file
>>
>> Thank you
>> Mamta Mohan
>>
>> I am listing below the contents of the mail one more time:
>>
>> Dear NAMD Team,
>>
>> I would like some help to resolve issues, I notice with simulation
>> which I ran on a system (1STN protein in cubic water box) for 10 ns.
>>
>> After I loaded psf and dcd file the following things I noticed:
>>
>> 1. Water box seemed deformed and with voids
>>
>> 2. protein coordinates seemed shifted inside the water box.
>>
>> After reading previous threads and inquiring (Please refer my mail to
>> Peter Freddolino in response to Thread
>> id: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8571.html),
>> I gathered that it could be that water density in not uniform and
>> causing deformation and voids in water box and a NPT should preceed
>> NVE phase to eliminate the issue. However I could not understand why
>> protein coordinates seems to have shifted.
>>
>> After examining the current system (that is system after simulation
>> psf+dcd file loaded as a molecule) a little closer against the system
>> before simulation (that is system before simulation psf+pdb file
>> loaded as a molecule), It seems after minimization the system origin
>> has shifted. Specifically water box seems to have shifted but protein
>> seems to have the same coordinates as before the minimization inside
>> the water box. I am listing the coordinates of the system from before
>> and after minimization below:
>>
>> Minmax, cellbasis vector and cellorigin
>>
>> Before minimization (wrap water on)
>>
>> minmax all {-30.2989997864 -14.7969999313 -17.797000885}
>> {38.7430000305 59.9790000916 47.3520011902}
>> CellBasisVector1 69.0419998169 0.0 0.0
>> CellBasisVector2 0.0 74.7760000229 0.0
>> CellBasisVector3 0.0 0.0 65.1490020752
>> CellOrigin 34.5209999084 37.3880000114 32.574501037613
>>
>> After minimization (wrap water on)
>>
>> minmax all {-31.4557056427 -13.0497903824 -15.8864183426}
>> {69.6460723877 75.5363922119 65.8884963989}
>> CellBasisVector1 101.10177803 0.0 0.0
>> CellBasisVector2 0.0 88.5861825943 0.0
>> CellBasisVector3 0.0 0.0 81.7749147415
>> CellOrigin 50.5508890152 44.2930912971 40.8874573708
>>
>> Second issue I noticed:
>> As simulation proceeds the protein seems to be drifting towards the
>> top of the water box. I am attaching snapshots I took at regular
>> intervals and they seems to point this clearly.
>>
>> Because of these two different but interrelated issues at the end of
>> the simulation water box seems deformed and with voids which I do not
>> think is the case at all.
>>
>> Please find listed below details of snapshot names. I took these snap
>> shoots at regular interval and they seems to point out what I think.
>>
>> snap_shot names I used:
>> protein_both_frm# - protein from molecule before simulation start
>> (that is ionized psf+pdb) and from simulated molecule (ionized
>> psf+dcd). Simulated molecule frame number # (1, 250, 500, 750, 1000).
>> This shows drift in protein. This is not very clear but one could see
>> that.
>>
>> water_box_only_both_frm# - water box from molecule before simulation
>> start (that is ionized psf+pdb) and from simulated molecule (ionized
>> psf+dcd). Simulated molecule frame number # (1, 250, 500, 750, 1000).
>> This show initially the water box origin has been moved but after that
>> it is maintained. However the later water box looks more deformed as
>> simulation progresses.
>>
>> waterbox_orig_protein_frm# - water box from molecule before simulation
>> start (that is ionized psf+pdb) and protein from simulated molecule
>> (ionized psf+dcd). Simulated molecule frame number # (1, 250, 500,
>> 750, 1000).
>> This clearly shows the drift of protein as simulation progresses.
>>
>> waterbox_frm# - water box and protein both from simulated molecule
>> (ionized psf+dcd). Simulated molecule frame number # (1, 250, 500,
>> 750, 1000).
>> This clearly shows that water box coordinates are maintained but
>> protein is drifting as simulation progresses.
>>
>> I am attaching my configuration file for reference. Along with
>> snapshots, PSF and PDB files are also included in the zipped folder.
>>
>> I would appreciate if you could point out what could be the reasons
>> for these apparent water box shift and protein drift and how can I
>> eliminate them.
>>
>> Thank you.
>> Mamta Mohan
>>
>> ----- Original Message -----
>> *From:* Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *To:* jim_at_ks.uiuc.edu <mailto:jim_at_ks.uiuc.edu>
>> *Cc:* Mamta Mohan <mailto:mamta_mohan_at_comcast.net>
>> *Sent:* Friday, October 31, 2008 6:54 PM
>> *Subject:* NAMD mail bounce problem.
>>
>> Dear Jim,
>>
>> I am sorry that message bounced and caused trouble.
>>
>> Currently I do not have a server where I can put my files and you can
>> look at them or download them.
>>
>> If there is a way you can suggest to help me out that would be very
>> helpful to me.
>>
>> I would look forward for your response.
>>
>> Thank you.
>> Mamta Mohan
>>
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>

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