VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Mar 03 2012 - 17:25:43 CST

On Sat, Mar 3, 2012 at 5:18 PM, siladitya mukherjee
<mukherjeesiladitya_at_gmail.com> wrote:
> Thanks for the earlier response. So for explicitly setting the box length
> for each frame, can I do something like this

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

> set n  [molinfo top get numframes]
>
> molinfo top set frame 0
> pbc set {1 1 1}
>
> molinfo top set frame 1
> pbc set {1.1 1.1 1.1}
>
> molinfo top set frame 2
> pbc set {1.2 1.2 1.2} etc.
>
> Thanks
>
>
> On Sat, Mar 3, 2012 at 2:45 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Sat, Mar 3, 2012 at 2:50 PM, siladitya mukherjee
>> <mukherjeesiladitya_at_gmail.com> wrote:
>> > Hi,
>> >
>> > I want to calculate the RDF of a system where cell volume changes with
>> > each
>> > frame, can I modify my tcl script like the following
>>
>> no. this script has syntax errors and doesn't make sense.
>> either you have a loop over the frames or set them explicitly.
>> but doing a loop with explicit setting of values is pointless.
>>
>> axel.
>>
>> >
>> > set n 50  [molinfo top get numframes]
>> > for {set i 0} {$i < $n} {incr i} {
>> >     molinfo top set frame 0
>> >     pbc set {1 1 1}
>> >     molinfo top set frame 1
>> >     pbc set {1.1 1.1 1.1}
>> >     molinfo top set frame 2
>> >     pbc set {1.2 1.2 1.2}
>> >     .......................
>> >    molinfo top set frame 50
>> >    pbc set {2 2 2}
>> > }
>> >
>> > Thanks
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.