[gmx-users] Pulling in GROMACS 4.0.3

[Johnny Lam]

Hi again,

I actually figured it out. Turns out, it was a stupid formatting error in
the .mdp file. Even though I had it as shown, it didn't read the pull
command because it wasn't formatted properly (thought it was still a part
of the first line). Sorry guys.

--Johnny

> Hi Justin,
>
> Thx for the reply. By pull apart, I just wanted to expose an 'activation
> site' by using a force. It is somewhat similar to pulling two domains of a
> protein away from each other. I'm not aiming to undo any secondary
> structure. I hope this is clearer. Thanks again!
>
> --Johnny
>
>
>>
>>
>> Johnny Lam wrote:
>>> Hi again,
>>>
>>>
>>> I am trying to pull apart a CG protein (to verify CG results with those
>>> of
>>> already published works using atomistic MD). Using the previous
>>> suggestions, my new pull code is the following:
>>>
>>
>> By "pull apart," do you mean to unwind the secondary structure of the
>> protein?
>> If so, I don't think it will work.  Doesn't MARTINI fix certain backbone
>> parameters such that secondary structure remains very rigid over time?
>>
>> If that's the case, then the vibrations you're seeing are just the
>> structure
>> trying to resist being pulled apart.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>
>
> -------------------------------------------------
> Johnny Lam
> ISPE Berkeley Chapter External Vice President
> Department of Bioengineering
> College of Engineering
> University of California, Berkeley
> Tel: (408) 655- 6829
> Email: johntus at berkeley.edu
>
>
>


-------------------------------------------------
Johnny Lam
ISPE Berkeley Chapter External Vice President
Department of Bioengineering
College of Engineering
University of California, Berkeley
Tel: (408) 655- 6829
Email: johntus at berkeley.edu