[AMBER] simulations in urea

From: <monica.imtech.res.in>
Date: Sat, 3 Jul 2010 17:44:38 +0530 (IST)

hi all;
i am simulating a protein dimer in 8M urea and i just want to have some suggestions
about the results if anybody has ever experienced.

few things i want to share are:
first: is the urea box a kind of slab distributed in parts means not a complete
box and oly after continuing simulations further it gets uniformed?
second: i expect my protein to unfold in 8M urea as i have seen in my solution
studies.so can i expect my dimer protein to be separated in monomers. i mean
shall i
remove periodic boundary or not?
by far upto 2ns i only observed some of the secondary structure distortions
thats it.

any help or any link to these kind of studies will be really commendable.
thanx in advance
hope to get reply from all


AMBER mailing list
Received on Sat Jul 03 2010 - 05:30:03 PDT
Custom Search