[gmx-users] how to set ref_t in .mdp---help!!
feenstra at chem.vu.nl
Thu Aug 12 18:01:31 CEST 2004
> Hello All:
> Since I want to simulate the force between proteins and graphite, I made a graphite file, including its .top and .gro files. This graphite can be calculated in vacuum. But in water, it always meet a problem. When I use mdrun program, it always stop suddenly, and report the error as follows:
> "Fatal error: ci = -2147483648 should be in 0 .. 4607 [FILE nsgrid.c, LINE 210]"
> And I found if I set the ref_t in .mdp file lower, the mdrun program can run more steps. For example, I set ref_t=50, it can run more than 10000 steps, but if I set ref_t=300, it just can run almost 200 steps.
> How can solve this problem? Because I want to run more than 200000 steps when ref_t=300.
You may have a badly equilibrated starting structure. Did you do energy
minimization of the graphite+water system? Do you use pressure coupling?
You could try to equilibrate for some time (~1-10ps) without pcoupl at
about the right density.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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