[gmx-users] understanding of difference between gromacs procedures

[Mark Abraham]

pragya chohan wrote:
> 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.

I don't understand what you mean by this.

> 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?

If one of you is position-restraining your lipids and one isn't, surely 
the fact that you get conformational change at a different time is expected.

You've also not said whether anybody is removing position restraints at 
any stage of the MD.

Mark