[gmx-users] how to set ref_t in .mdp---help!!

[Anton Feenstra]

yinjun wrote:

> 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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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