Re: Protein in/out of box

From: Monika Sharma (mon_sharma_at_research.iiit.ac.in)
Date: Mon May 28 2007 - 11:23:38 CDT

Yes.. That was the main concern. I looked at the archive earlier also
and saw that everyone seemed concern to look for protein going out.
Instead I wanted my protein to be in. So wanted to know if rmsd and rgyr
calculation might pose some problems. Thanks all of you for prompt reply.
Cheers!!

===================
Life is all about exploration....
===================
Gianluca Interlandi wrote:

>Actually, you don't need to unwrap the coordinates if you only have to
>calculate things like the root mean square deviation (RMSD) and you have
>only one protein in your system. It is enough to align your protein with
>the first frame along your simulation. How to rms align a protein with VMD
>is described in:
>
>http://www.ks.uiuc.edu/Research/vmd/current/ug/node185.html
>
>and the subsections linked there.
>
>Hope this helped,
>
> Gianluca
>
>On Mon, 28 May 2007, Gianluca Interlandi wrote:
>
>
>
>>Yes, this is normal. Please, see older NAMD list threads to unwrap the
>>coordinates:
>>
>>http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5714.html
>>
>>http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5716.html
>>
>>Gianluca
>>
>>On Mon, 28 May 2007, Monika Sharma wrote:
>>
>>
>>
>>>Dear All,
>>>I am doing 10ns simulation (production run) of a small protein. The run as
>>>such seems to be going fine. But when I am viewing the dcd file in VMD, it
>>>seems that the protein tries to diffuse out of the solvent box. A good portion
>>>of it can be seen out of the box, and then it moving from one edge of the box
>>>to other, and then wrapping back. The trajectory looks so weird that the
>>>protein goes out from one edge; move to another edge in next frame, then again
>>>come back to the former edge and wrapped back. It can be seen happening 3-4
>>>times during 10 ns run. Now my question is that ; Does it indicate that
>>>results are not reliable (because then i may be looking for rmsd and rgyr
>>>plots which will depend upon the alignment of the frames), or is it a routine
>>>thing that happens with longer simulations and i can go ahead with my
>>>results?? (because this is the longest simulation I have given till now). or
>>>Can there be any option to remove these discrepancies in the run? I am using
>>>wrapAll on, wrapNearest on in the conf file. If anybody can help me out...
>>>Thanks in advance
>>>Regards,
>>>Monika
>>>
>>>===========================
>>>Life is all about exploration....
>>>===========================
>>>
>>>
>>>
>>-----------------------------------------------------
>>Dr. Gianluca Interlandi gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> +1 (206) 714 4303
>> http://biocroma.unizh.ch/gianluca/
>>
>>Postdoc at the Department of Bioengineering
>>at the University of Washington, Seattle WA U.S.A.
>>-----------------------------------------------------
>>
>>
>>
>
>-----------------------------------------------------
>Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
>Postdoc at the Department of Bioengineering
>at the University of Washington, Seattle WA U.S.A.
>-----------------------------------------------------
>
>
>

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