[gmx-users] few doubts regarding 1-4 interaction

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 30 17:03:19 CEST 2009

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?


> 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.


> Can you please tell me your suggestion on these??
> Thank you. Aswathy
> Dept. Biotechnology Ext. 3108 _______________________________________________
>  gmx-users mailing list    gmx-users at gromacs.org 
> http://lists.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
> gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php


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


More information about the gromacs.org_gmx-users mailing list