[gmx-users] large force on an atom

[Samik Bhattacharya]

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 



1015   

 

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.
Thank You
Shamik






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Re: [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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--


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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