[gmx-users] large force on an atom

[Justin A. Lemkul]

Samik Bhattacharya wrote:
> hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using 
> inflategro perl script. just after the first run when i'm running grompp 
> to minimize it i have found a large force on a phenylalanin atom which 
> is well over 10^15   ^ Now what to do with this one?  I had a view of 
> that particular atom through pymol which is an Oxygen (CO). Right now 
> I’m a little anxious that if I keep this and go on it’ll affect the 
> future steps. Any suggestions regarding this will be very encouraging..

Well, is that atom clashing with something else in your system?  The only way I 
can think to get a force of 10^15 is substantial atomic overlap.

-Justin

> Thank You
> Shamik
> 
> 
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-- 
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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

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