[gmx-users] Re: mdp file problem

[Justin A. Lemkul]

madhumita das wrote:
> Dear Justin,
> 
> I could solve that perticular error but another problem has come, After 
> running energy minimization, the sulphur and mercury(GG)atoms (present 
> in the modified residue of cysteine named CYP at 182 position) break the 
> bonds.
> 

Bonds don't break and form during molecular mechanical processes.  Likely 
whatever you're seeing is simply extreme instability in the system.  Most likely 
your topology is wrong.  You haven't said what parameters you're using, but as I 
know I have indicated previously, deriving good parameters for such an exotic 
species will be extremely challenging for the biomolecular force fields present 
in Gromacs.  My guess is that you haven't yet obtained proper parameters.

-Justin

> On Thu, Nov 10, 2011 at 7:28 PM, madhumita das 
> <madhumita.bioinfo at gmail.com <mailto:madhumita.bioinfo at gmail.com>> wrote:
> 
>     Dear Justin,
> 
>     I could resolve that perticular error but another problem has come,
>     After running energy minimization, the sulphur and mercury(GG)atoms
>     (present in the modified residue of cysteine named CYP at 182
>     position) break the bonds and become freely moving atoms. I have
>     attached my prepared gromacs(aqp_newbox) topology(topol.top) and
>     file obtained after energy mimization(em.gro).
>                                                         Please help me.
>                                                                                                       
>     Madhumita
> 
> 
>     On Tue, Nov 8, 2011 at 5:03 PM, madhumita das
>     <madhumita.bioinfo at gmail.com <mailto:madhumita.bioinfo at gmail.com>>
>     wrote:
> 
> 
>         Hi GROMACS users,
> 
>             i am in the midst of simulating  a protein in water.  I have
>         modified  a residue  in my  pdb file at position  182,  using
>         amber and then acpype.py.  But  after running  the energy
>         minimization step,using  em.mdp file  generated from acpype ,
>         following error comes.
> 
>         Steepest Descents:
>            Tolerance (Fmax)   =  1.00000e+03
>            Number of steps    =         5000
>         Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=        
>         inf, atom= 2700
>         Stepsize too small, or no change in energy.
>         Converged to machine precision,
>         but not to the requested precision Fmax < 1000
> 
>         Double precision normally gives you higher accuracy.
> 
>         writing lowest energy coordinates.
> 
>         Steepest Descents converged to machine precision in 18 steps,
>         but did not reach the requested Fmax < 1000.
>         Potential Energy  =  9.8982703e+17
>         Maximum force     =            inf on atom 2700
>         Norm of force     =  1.7474532e+19
>          The mdp file is attached.
> 
>                                            Please help.
>                                                                                                                                                                                        
>         Madhumita Das
> 
> 
> 

-- 
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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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