[gmx-users] energy minimisation of Si3N4 did not converge

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 25 12:57:26 CET 2010

Kothai Thiruvengadam wrote:
> Dear all,
> I am using MD simulation of a protein on Silicon nitride surface. The 
> surface has been created using VMD and tcl script (ref. bionano 
> tutorial).The protein+surface complex also has been generated using 
> VMD.Using that PDB file I have done md simulation in gromacs. One itp 
> file for silicon nitride has been developed using PRODRG server and 
> included in the top file.
> But, during energy minimisation  I got a message
> Steepest Descents did not converge to Fmax < 8000 in 2001 steps.
> Potential Energy  = -4.5347610e+06
> Maximum force     =  1.0913173e+05 on atom 7417
> Norm of force     =  2.8918979e+02
> The EM ends without converging to Fmax. I put different  values of Fmax 
> and steps starts from 1000. But for  Fmax 8000 and  2000 steps also I am 
> getting the same message. What force field I can use for Silicon nitride 
> surface? How can I rectify this error?

The unmodified output of PRODRG often contains undesirable and inconsistent 
charges/charge groups (when compared to known functional groups in a given force 
field).  Thus the topologies from PRODRG, while useful as a starting point, 
often require manual modification.

In the case of something like Si3N4, you certainly have your work cut out for 
you.  The Gromos96 force fields, like all of natively supported by Gromacs, were 
designed for simulations of biomolecules, so their application to other 
materials may or may not be straightforward.  That doesn't mean you can't make 
it work, but you will probably have to go into the literature to see how people 
have come up with parameters for their materials, since Gromacs has certainly 
been used to simulate non-biological systems (CNT, silica, etc).


> - T.Kothai
> Centre for Biotechnology
> Anna University Chennai


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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