On Jan 22, 2009, at 6:38 AM, li jianguo wrote:
Dear all,
I am running MD simulaiton using Gromacs for alpha-helilx
polyalanine solution. The initial configuraiton of polyalanine
peptide was generated using Discovery Studio. I follow the procedure
below:
1: solvate the polyalanine in a water box
2: energy minimization (steep for 5000 steps and cg for some steps
until convergence)
3: position restraint MD for 200 ps in NVT
4: position restraint MD for 200 ps in NPT
After that, I run MD simulation. The strange things is that the
alpha-helix polyalanine melt during MD simulation, and it became
random coil after several nano seconds.
Did any one encount such problem?
I would indeed expect a polyalanine peptide to be mostly unstructured
in solution.
I seem to me that the length of the polyalanine would be a very
important factor
to the "structure" of the polyalanine peptide. I believe there is some
experimental
data on this.
The force field you use is also important. For short peptide different
FF would have
different propensity for helix/shift.
Thanks very much,
Jianguo
Dept. Chemcial and Biomolecular Engineering
National University of Singapore
_______________________________________________
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
_______________________________________________
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
