[gmx-users] Simulation box explodes

[David van der Spoel]

Robson Peguin wrote:

> Hi Gromacs Users,
>
> I'm trying to simulate an interface in Gromacs composed by water and 
> hydrofluoroalkane (HFA). However, during the energy minimization, my 
> simulation box explodes from the hydrofluoroalkane side. I tried a 
> couple of things, such as: decrease LJ parameters (HFA), decrease 
> atomic charges (HFA), decrease temperature, increase the molecular 
> weight of the H atom, decrease time step, run in NPT & NVT... However, 
> I wasn't able to solve the problem. If you someone has any 
> suggestions, they are more than welcome.


Could you have unit problems (Angstrom - nm) or something like that?
Alternative method could be to reduce the density (editconf) by 0.5 or 
so, minimize and do MD with slow pressure coupling.

>
> Thank you very much
>
> Robson Peguin
>
> -- 
> Robson Peguin, PhD Student
> Wayne State University, ChE
> Detroit - MI, 48201 - USA
> 2015 MEB, (313) 577-1416
> 2348 ENG, (313) 577-5765
> Fax: (313) 577-3810
> e-mail: robson_peguin at wayne.edu <mailto:robson_peguin at wayne.edu>
> http://chem1.eng.wayne.edu/~sdr/ <http://chem1.eng.wayne.edu/%7Esdr/>
>
>
> -- 
> Robson Peguin, PhD Student
> Wayne State University, ChE
> Detroit - MI, 48201 - USA
> 2015 MEB, (313) 577-1416
> 2348 ENG, (313) 577-5765
> Fax: (313) 577-3810
> e-mail: robson_peguin at wayne.edu <mailto:robson_peguin at wayne.edu>
> http://chem1.eng.wayne.edu/~sdr/ <http://chem1.eng.wayne.edu/%7Esdr/>
>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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