Kavyashree M wrote:
Dear users,
I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of 50001 data points,
282 are <= 1.4nm
280 are < 1.4nm
144 are < 1.3nm
79 are < 1.2nm
28 are < 1.1nm
4 < 1.0nm
I agree that this is quite wrong but I wanted to know whether
any useful information can be gathered out of this simulation?
Not likely. Nearly 2% of the saved frames are unusable, indicating that
potentially even more of the frames in the trajectory are useless, as well, and
the dynamics that produced them are flawed.
In another data while calculating the energy terms it gives
nan (not a number error) for rmsd alone eg -
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 300 9e-05 -nan -0.000501989 (K)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 0.99914 0.027 -nan 0.0174391 (bar)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Volume 517.755 0.0094 -nan 0.010871 (nm^3)
Initially i though some data points are missing but later
gmxcheck gives that all the data points are present.
now what could be the error?
I had asked this question before and was instructed to check the
trajectory. I checked the rmsd rmsf of this with the other proteins
it similar but one of the segment has high rmsf compared to the other
proteins.
My advice to you was to *watch* the trajectory to see where the PBC violations
occurred, not run more analysis. I doubt RMSF and RMSD will tell you anything
useful.
No one's been able to diagnose the problem based on this (continually posted)
information. If it's a useless trajectory, why bother?
-Justin
Thanking you
With regards
M. Kavyashree
--
========================================
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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