VMD-L Mailing List
From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Sun Jun 21 2015 - 03:55:15 CDT
Thanks Panagiotis. I cannot make it work. First I am dealing with a
membrane-in-water system and no protein is involved. (It does not work by
changing the selection text either. Just nothing happens after pressing
enter. ) Then RMSD trajectory tools do no difference neither.
On Sun, Jun 21, 2015 at 4:41 PM, Panagiotis Lagarias <
> Dear Kevin,
> I think you should try these steps (at least here it seems to work well,
> but you know better):
> 1) pbc wrap -centersel protein -center com -compound res -all (write it on
> tk Console: Extensions > Tk Console )
> 2) Extensions > Analysis > RMSD trajectory tools > ALIGN.
> Is it OK now?
> On Sun, Jun 21, 2015 at 10:56 AM, Kevin C Chan <
> cchan2242-c_at_my.cityu.edu.hk> wrote:
>> Dear Users,
>> I am confused by the options of the PBC tool. Currently I have last frame
>> of a membrane in water simulation. As I have turned on "Wrap ALL" during
>> simulation, the system "trapped" inside a box and now water is in the
>> middle of the box and two layers of membrane are splitted into the top and
>> bottom. I would like to unwrap this thing back to my initial configuration
>> - two-layer in the middle and water above and below so what should feed to
>> pbc unwrap?
>> I have made tons of trials and still cannot work out. I will appreciate
>> any help.
>> Thanks in advance,
>> City University of Hong Kong