[gmx-users] CG-MD simulation of protein, always crash with protein

[Martti Louhivuori]

On 15 Apr 2010, at 18:06, Trang wrote:
> My target system is a protein with lipid molecules added randomly  
> (using GENBOX). Running MD, I expect to

I hope you're using a larger van der Waals distance (0.24nm or so)  
when inserting the lipids.

> broke down the problem, that is, to run md simulation for the  
> protein molecule only, and in vacuum. Still no improvement. Although  
> all the distances in the minimized structure are visually proper,  
> the system exploded.

If you can't run the protein even in vacuum, then the problem is  
either in your MD parameters, starting co-ordinates or some simple  
mistake somewhere. Since the .mdp files you posted seem ok, my bet is  
on the starting co-ordinates, just as Xavier proposed.

Could you post the system topology (.top) and the protein topology  
(.itp), so we can rule out any mistakes in those? You should also  
double check whether you have close contacts between some atoms in the  
protein; e.g. in VMD this is easily done using the "dynamic bonds"  
representation.

-martti-
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Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
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