[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..

[Yu Ogawa]

Dear Mark,

At the very last part of the log file I can find outputs at 0.0 ps, but
nothing more below.

> Have you equilibrated your system first? Does another integrator or
thermostat work?

Yes, my mdrun program works with the other inputs, and I think the initial
structure is equilibrated enough because I can run a NPT simulation
properly with this structure file with md integrator and berendsen
thermostat.

I also tried the similar calculation with md integrator and Nose-Hoover. In
this case I could start running the simulation, but the temperature was not
controlled, and it stayed around the value of gen_temp.

Thank you,
Yu


2014-05-23 16:33 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> First, find something out. Does the installation work for any other
> simulation? What does the log file say? Have you equilibrated your system
> first? Does another integrator or thermostat work?
>
> Mark
>
>
> On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa <ayogwa at gmail.com> wrote:
>
> > Hello gmx-users,
> >
> > I tried to run a simulation to calculate a specific heat capacity of
> > infinite molecular crystal with the md-vv integrator and Nose-Hoover
> > thermostat on ver 4.6,
> > but it crashed immediately with only the message of Segmentation fault.
> >
> >
> > Does anyone have a similar experience or any good ideas for this
> problems?
> >
> > I would appreciate very much if somebody gives any comments on this
> matter.
> > Thank you,
> >
> > Yu
> >
> > Yu OGAWA, PhD
> > Cermav-CNRS, Grenoble, France
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