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

[Mark Abraham]

What has gen_temp to do with it? You sound like you're doing an
equilibration, then generating velocities at gen_temp, then running with a
thermostat with a different ref_t from gen_temp. Why?

Mark


On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa <ayogwa at gmail.com> wrote:

> 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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