[gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

hello gmx users
I am doing a simulation of protein in membrane after simulating a protein in water and inserting it into a membrane. One of my lab-mates is doing the same system by following a different procedure (difference listed below)
I did position restrain by define = -DPOSRES -DPOSRES_LIPID
 and he is doing define = -DPOSRES
 and then for lipid. 
Rest of the procedure is the same. 
He got conformational change within 250 ps and I did not get till 2ns 
even though we use same parameters on mdp and have same starting structure.
 
Can anyone give some insight what may be the logic for this difference?
 
I can send gro files off the list for anyone willing to help.
 
Thanking You
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