Re: [gmx-users] Pull Code constant value

[Vytautas Rakeviius]

I suggest trial and error in quite short runs without wasting time on waiting 
for next day or so. Really large k can create segmentation faults or 
"cannonball into wall" like effects in MD movie.
 

On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary 
 wrote:
 

 Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?

Thanks,

Souparno Adhikary
University of Calcutta.
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[gmx-users] Pull Code constant value

[Souparno Adhikary]

Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?

Thanks,

Souparno Adhikary
University of Calcutta.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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