Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Tue Jan 30 2007 - 19:41:01 CST

Hi Won-Young,
The VMD script library has tools (PBCTools & PBCWrap) that can be
used to visualize periodic boundary conditions and wrap a set of
atoms around them for visualization. I think this should help you.
-Tim

http://www.ks.uiuc.edu/Research/vmd/script_library/

On Jan 29, 2007, at 3:56 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:

> Thanks for the help, Tim.
>
> I have used the wrapWater option in the MD simulation.
> So, the dcd file is already created.
>
> In this case, how can I visualize the system with all the waters in
> a box using VMD?
>
> Won-Young
>
> ---- Original message ----
>> Date: Mon, 29 Jan 2007 15:04:22 -0600
>> From: Timothy Isgro <timisgro_at_ks.uiuc.edu>
>> Subject: tutorial-l: Re:
>> To: "<wahn_at_uiuc.edu>" <wahn_at_uiuc.edu>
>> Cc: tutorial-l_at_ks.uiuc.edu
>>
>> Hi Won-Young,
>> By specifying "wrapWater on" in your NAMD configuration file, NAMD
>> will wrap the coordinates of water molecules. "wrapAll" and
>> "wrapNearest" provide similar functionality.
>>
>> From the NAMD User's Guide (http://www.ks.uiuc.edu/Research/namd/
>> current/ug/) under "Periodic boundary conditions":
>> # wrapWater < wrap water coordinates around periodic boundaries? >
>> Acceptable Values: on or off
>> Default Value: off
>> Description: Coordinates are normally output relative to the way they
>> were read in. Hence, if part of a molecule crosses a periodic
>> boundary it is not translated to the other side of the cell on
>> output. This option alters this behavior for water molecules only.
>>
>> # wrapAll < wrap all coordinates around periodic boundaries? >
>> Acceptable Values: on or off
>> Default Value: off
>> Description: Coordinates are normally output relative to the way they
>> were read in. Hence, if part of a molecule crosses a periodic
>> boundary it is not translated to the other side of the cell on
>> output. This option alters this behavior for all contiguous clusters
>> of bonded atoms.
>>
>> # wrapNearest < use nearest image to cell origin when wrapping
>> coordinates? >
>> Acceptable Values: on or off
>> Default Value: off
>> Description: Coordinates are normally wrapped to the diagonal unit
>> cell centered on the origin. This option, combined with wrapWater or
>> wrapAll, wraps coordinates to the nearest image to the origin,
>> providing hexagonal or other cell shapes.
>>
>> -Tim
>>
>> On Jan 29, 2007, at 1:42 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:
>>
>>> Dear NAMD users,
>>>
>>> I ran a molecular dynamic simulation in a NVT ensemble with NAMD.
>>>
>>> When I tried to examine the trajectory with VMD, I noticed that
>>> some water molecules are located outside of the periodic box. Is
>>> that possible? If it is possible, how can I wrap all water
>>> molecules in a periodic box.
>>>
>>> Thanks,
>>>
>>> Won-Young
>>>
>>> **
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>>> majordomo
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>>

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