[gmx-users] Protein distance with respect to box walls

[Erik Marklund]

Hi,

The location of the box boundary is irrelevant in virtually all cases, unlike the distance to the periodic image. Why do you need to know the distance to the box? Note that regardless of box angles the simulation cell will be represented as a cuboid within mdrun anyway.

Erik

On 9 Dec 2014, at 16:55, xu zhijun <simulationxu at yahoo.com> wrote:

> Try to use the VMD to directly measure the distance between the protein and box boundary. 
> 
> 
>     On Tuesday, December 9, 2014 8:16 AM, "Smith, Micholas D." <smithmd at ornl.gov> wrote:
> 
> 
> Hi James,
> 
> The utility g_mindist lets you measure the minimum distance between a selection and its periodic image, if what you are trying to do is just confirm that your simulation box is large enough to prevent periodic image effects, this is one way to check.
> 
> Kind Regards,
> 
> Micholas
> 
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> 
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of amin at imtech.res.in <amin at imtech.res.in>
> Sent: Monday, December 08, 2014 11:39 PM
> To: Gmx users
> Subject: Re: [gmx-users] Protein distance with respect to box walls
> 
> Dear James,
> 
> I think if you load your system in VMD you can measure the dimensions of
> protein with something like
> 
> set sel [atomselect top "protein"]
> 
> measure minmax $sel
> 
> Regards.
> 
> Amin.
> 
> On 2014-12-09 08:55, James Lord wrote:
> 
>> Dear Users,
>> I have a protein in a box and was wondering to know how to figure out the
>> protein distance to the box walls? I can see the box dimensions at the end
>> of .gro file but how to know what is (x,y,z) of protein in the box?? any
>> comments?
>> Cheers
>> James
> 
> 
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