[gmx-users] position restraint....NEED URGENT HELP

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 14 13:30:34 CEST 2010

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:


> Here is .top file that i am using:


> rlist = 2.0
> coulombtype = PME
> rcoulomb = 2.0; in nm units
> vdwtype = cut-off
> rvdw = 2.0


> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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