[gmx-users] Re: System exploided befor runing

[Vitaly Chaban]

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gurgo> I have a following problem. Last time I send it to gromacs user but I
gurgo> couldn't get proper reply.
gurgo> I make the solution box of organic solvent. It is homeogen and mixed
gurgo> properly.
gurgo> It also has a minimum energy. I put one protein in this solution. Before
gurgo> put the protein in the solution I minimimized it also. Now I mixed 2
gurgo> system which each of them are minimized. After put the protein in the
gurgo> solution I try first to minimized it then run it but unfortunately it
gurgo> crashed. It did not work at all. I also tried to run the system without
gurgo> minimization but it also did not work at all. I try with opls forcefield
gurgo> also (I guess maybe the proble is from forcefield) but it also did not
gurgo> work. After runing befor starting to run or minimization (no difference) I
gurgo> faced with following message:


What tool did you use to mix those two systems? Also, try to modify
the parameters of energy minimization (in mdp) and to decrease a
timestep (in mdp) for some first ps of your run.

Visualize the pdb files created after crash to realize where the problem can be.


Every time I found this problem in my practice is was due to the particle
intersections and thereby huge energies in the system.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698