VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Thu Nov 24 2016 - 19:55:32 CST

Hello Jerome

I am getting the error below while running the make:

g++ -fpic -O3 -I/usr/include/tcl -c -o qwrap.o qwrap.cpp
qwrap.cpp:1:17: fatal error: tcl.h: No such file or directory
compilation terminated.
<builtin>: recipe for target 'qwrap.o' failed
make: *** [qwrap.o] Error 1

And this one while running on Tcl:

package require qwrap
couldn't load file "qwrap.so": qwrap.so: cannot open shared object file: No
such file or directory

Please let me know how to fix it or I missed some step?

Thanks and regards
Sourav

On Sat, Nov 19, 2016 at 11:46 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Norman and everyone,
>
> A quick unwrapping feature is now available as "qunwrap".
> https://github.com/jhenin/qwrap
>
> Please give it a spin and let me know what you think!
>
> Jerome
>
> On 17 November 2016 at 10:09, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi Norman,
>>
>> You are not the only one to request such a feature. I'm definitely going
>> to implement that, but not as "remove long bonds", which is cumbersome and
>> is done by "pbc join" in PBCTools, but rather what I implemented in "pbc
>> unwrap", that is, remove large jumps from one frame to the next. That
>> requires a more or less continuous trajectory starting from a "clean"
>> configuration where all the fragments are in one piece.
>>
>> Jerome
>>
>>
>>
>> On 17 November 2016 at 09:05, Norman Geist <norman.geist_at_uni-greifswald.d
>> e> wrote:
>>
>>> Hey,
>>>
>>>
>>>
>>> thanks for your work so far. Would it be difficult to also implement a
>>> unwrap function (more or less remove long bonds)? Since f.i. GROMACS
>>> outputs trajectories always wrapped.
>>>
>>>
>>>
>>> Norman
>>>
>>>
>>>
>>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *Jérôme Hénin
>>> *Gesendet:* Mittwoch, 16. November 2016 14:55
>>> *An:* VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>> *Betreff:* vmd-l: Fast PBC wrapping in VMD
>>>
>>>
>>>
>>> Hi everyone,
>>>
>>>
>>>
>>> This is a reminder that there is a faster alternative to pbc wrap from
>>> the PBCTools plugin, in the form of qwrap:
>>>
>>> https://github.com/jhenin/qwrap
>>>
>>>
>>>
>>> It has improved since the last time I mentioned it on this list,
>>> specifically, you can now restrict the wrapping to a given selection, as in
>>> (my personal favorite):
>>>
>>> qwrap sel "not protein" center protein
>>>
>>>
>>>
>>> Thanks to a contribution by Giacomo Fiorin, wrapping can also be done
>>> based on VMD fragments.
>>>
>>>
>>>
>>> Qwrap is written in C and is relatively simple-minded, hence the speed.
>>> The main limitation with respect to pbc wrap is the treatment of
>>> orthorhombic cells only - however that can change in the future.
>>>
>>>
>>>
>>> As usual, feedback is welcome.
>>>
>>>
>>>
>>> Jerome
>>>
>>
>>
>