VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Mar 12 2015 - 04:22:55 CDT

Thanks for the hints.

I used “Wrapall on” for my simulation so I guess it wrapped all atoms and is equivalent to something like “-center com -centersel protein” for "pbc wrap". So I did try -center com and -center bb for "pbc box" and they both work perfectly fine. I was just wondering why "-center unitcell" went wrong even after I read in the correct xst file. I was just worried I made mistakes somewhere when defining the PBC for my simulations. So what was “-center unticell” trying to draw?

Thanks in advance,
Kevin
> On 12 Mar, 2015, at 15:27, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
>
> If you wrapped using f.i. “-center com” you need to use the same parameters for “pbc box”.  <>
> Example:
>
> pbc box -center com -centersel protein
>
> or what usually works out fine:
>
> pbc box -center bb -centersel all
>
> Norman Geist.
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Josh Vermaas
> Sent: Wednesday, March 11, 2015 5:08 PM
> To: Kevin C Chan; VMD Mailing List
> Subject: Re: vmd-l: PBC Plugin
>
> Hi Kevin,
>
> Does "pbc get" give you what you expect? I suspect what is happening is that it is drawing a box of the correct size, but at the wrong origin. I don't typically draw the boxes, so someone else may have more info, but I suspect if you recentered the trajectory so that it is centered on the origin, the box will encompass your trajectory.
>
> -Josh Vermaas
>
> On 03/11/2015 10:09 AM, Kevin C Chan wrote:
>> Dear Users,
>>
>> I am currently confused by the pbc plugin shipped with VMD 1.9.2. I have executed the following steps:
>>
>> mol new ionized.psf
>> mol addfile npt-1.dcd
>>
>> pbc readxst npt-1.xst
>> pbc box
>>
>> However, on the OpenGL display, it gives a box besides my system. I have checked my PBC parameters by drawing a sphere at the box centre manually read from the xst file and it is lying at the centre of my system. I have no idea what could be possibly wrong to cause a box appearing at another unexpected position (few nm away).
>>
>> Thanks in advance,
>>
>> Kevin
>> PhD Candidate
>> Department of Physics and Material Science
>> City University of Hong Kong
>> ukevi_at_gmx.hk <mailto:ukevi_at_gmx.hk>
>>
>