[gmx-users] understanding of difference between gromacs procedures
Mark.Abraham at anu.edu.au
Mon Mar 17 12:16:29 CET 2008
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.
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