[gmx-users] Re: Regarding Gromacs problem

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 25 15:33:18 CEST 2009

Please do not send private emails asking for help.  I've said this dozens of 
times; it is much more beneficial to the community as a whole to post the 
gmx-users list, where discussions are archived for future use.  You also have a 
better chance of reaching someone who knows how to solve your problem.  I know I 
respond a lot, but I don't always have an answer, nor do I advertise myself as a 
private tutor.  Contribution to the list is voluntary, when I've got a few moments.

Your system is blowing up, a fairly common problem.  See here for general tips:


rituraj purohit wrote:
> Hello Justin..
>  I am getting a problem during dynamics(position restrain) of pr.mdp,
>  at first i given dt = 0.002 and for 200ps (because protein is very big
>  having 1480 aa = 11058 atoms) shows an error called table size at 1.6
>  ps. Then i changed it dt = 0.001 for 200ps, but again i had a same
>  error at ~45 ps.
>  So finally i giving dt = 0.0001 for 200 ps, now its moving fine..but
>  steps become 20 lacks :(
>  1) The correction which i done , is it ok?

You're probably just prolonging the inevitable; the system is not stable.

>  2) Is error occurred (with dt = 0.002 & 0.001) due to big size of protein?

No; it is due to some physically unrealistic aspect of the model physics 
(unresolvable clashes, inappropriate parameters).  Size should not be a problem; 
people are simulating viral capsids nowadays.

>  3) To do dynamics for such a big protein is rel event?

That's up to you.

>  4) Is 200 ps enough for this protein? is their any relation between
>  protein size and pre-equilibrium period ?

There is no standard rule, really.  To justify equilibration, your observables 
have to have converged (i.e., temperature, pressure, density, RMSD, etc).


> Please help me in this..
>  Regards,
>   Rituraj


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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