[gmx-users] Re: System exploided befor runing

Vitaly Chaban chaban at univer.kharkov.ua
Mon Sep 15 08:24:45 CEST 2008

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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

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