nikhil damle wrote:
Hey !
My doubt posted few days back still holds. I am trying to simulate the
kinase domain in complex with cyclin. when i keep entire complex either
position restrained or flexible, MD runs without any errors. But as soon
as i keep cyclin position restrained keeping kinase domain flexible, it
gives errors.
Initially it gave LINCS warnings saying fatal error that charged group
at atom xxxxxx moved more than distance allowed by DD in direction X.
Error persists even if i repeat the same procedure this time
equilibrating the system for 150ps instead of usual 40ps. the pdb file
obtained after equilibration appears perfect without any breaks.
As suggested by Justin, I also tried to check if my system is blowing
up. But when i take co-ordinates of last frame, i get few random
fragments having no 3D structure/ interconnections.
That is not what I suggested. I said to watch the trajectory to see where it
starts to break down. If it's already broken, you can't see where the problems
started. Also:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Here is .top file that i am using:
<snip>
rlist = 2.0
coulombtype = PME
rcoulomb = 2.0; in nm units
vdwtype = cut-off
rvdw = 2.0
<snip>
I wish to do MD with increased electrostatic and VdW cut-offs. Chain B
is Cyclin and A is kinase domain.
Why do you wish to increase the cutoffs? For rvdw especially, you may be
seriously breaking the force field.
If you're restraining one species and altering the nature of the surrounding
interactions, you may be preserving or creating clashes that cannot be resolved
because of the restraints. See the above link for tips on how to better
diagnose what's going on.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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