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 - 13:48:49 CST

----- Original Message -----
From: "Mamta Mohan" <mamta_mohan_at_comcast.net>
To: "Peter Freddolino" <petefred_at_ks.uiuc.edu>
Cc: <jim_at_ks.uiuc.edu>; <namd-l_at_ks.uiuc.edu>
Sent: Monday, November 10, 2008 2:39 PM
Subject: Re: namd-l: Simulation issues: water box deformation after
minimization and shifting protein coordinates during production run

> 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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