[gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 11 12:37:21 CET 2011

On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:
> Sorry, in previous mail i did not write md protocol in details what i
> followed for simulation. after energy minimization steps i did PR for 200
> ps and then run the production MD. Even i did vacuum energy minimization
> before adding solvent for all systems. I used steep followed by cg for
> prot-solvent energy minimization which reached up to minimum applied force
> 100 KJ/mol/nm.

Your results suggest you did not equilibrate well enough. See the link I 
gave last time.


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