Ms. Aswathy S wrote:
Hi gromacs users,
I am facing the same error during Production run that faced by so many
gromacs users and I know this query has been answered for several times. But
Could you please tell me some specific doubt regarding the 1-4 interaction
error that usually occurs?
I have equilibrated my protein ligand system of around 600 ps and shown a
satisfied level of equilibration. Then I moved to the Production run of 3ns.
But shows the same 1-4 interaction error. My doubts are,
1. It was advised by gromacs experts that better I should go for another
round of minimization. Is it on the equilibrated structure?
It would be good if you could remind us of what you are doing, as well as cite
the actual post where you were told to do this.
2. If so Do i need to equilibrate again after minimization?
Yes.
3. I have did 2500 steps of minimization on the structure which is
equilibrated and then again run for 3ns production run But occured the same
error at 3 lakh step? if I reduce my time step how that will affect this
error(I have seen in the error section of gromacs that another possibility is
to reduce the time step?)
Reducing the timestep can in some cases finesse the problem into behaving. If
there is something more deeply wrong with your model, then this probably won't
help out a whole lot.
If you can post a more complete description of what it is you are doing, what
parameters you are using, etc. you might get more detailed suggestions. The
bottom line is, if your system is blowing up, something about the model physics
is unreasonable.
-Justin
Can you please tell me your suggestion on these??
Thank you. Aswathy
Dept. Biotechnology Ext. 3108 _______________________________________________
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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