VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 21 2014 - 15:23:29 CDT

please always copy the mailing list on your replies.

On Fri, Mar 21, 2014 at 4:21 PM, Kipp Johnson <kippjohnson_at_uchicago.edu> wrote:
> Hi Axel,
>
> Thank you so much for your help. I really appreciate it.
>
> It looks like it's working now. My two commands were:
>
> pbc unwrap -first 0
> pbc wrap -centersel protein -center com -compound fragment -all
>
> As a sanity check, does that look reasonable to you?

does the resulting trajectory look reasonable to you? are structural
properties (like g(r)) unchanged.

axel.

>
> Best,
> Kipp
>
>
>
> On Tue, Mar 18, 2014 at 1:10 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Mar 17, 2014 at 7:08 PM, Kipp Johnson <kippjohnson_at_uchicago.edu>
>> wrote:
>> > Dear VMD List,
>> >
>> > I am interested in analyzing the water around a protein in a NAMD
>> > simulation
>> > where the protein has multiple chains and some of the chains move out of
>> > the
>> > box during the simulation.
>> >
>> > I unwrapped the system with the command "pbc unwrap -first 0". This
>> > works
>> > well for the protein, which is correctly unwrapped. However, the waters
>> > do
>> > not behave as expected. At the first frame, they all remain inside of
>> > the
>> > water box and periodic boundary limits. However, as the trajectory
>> > continues, they spread outside of the water box and form a low-density
>> > sphere around the protein.
>> >
>> > Here are pictures describing what I am observing after I unwrap the
>> > trajectory:
>> >
>> > Before: http://home.uchicago.edu/~/kippjohnson/protein_frame1.png
>> > After: http://home.uchicago.edu/~/kippjohnson/protein_frame2.png
>> >
>> > Can anyone offer suggestions on how to correctly unwrap this?
>>
>> you did the unwrapping correctly, but now you have to wrap it again,
>> but with -compound fragment to keep molecules intact and centered on
>> the protein.
>>
>> axel.
>>
>> >
>> > Thank you,
>> > Kipp Johnson
>> >
>> >
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.