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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
