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

[Yu Ogawa]

Sorry for my poor explanation. I tried to simulate a temperature rising
process from 0 K to 500 K.
At first I did a simulation with gen_vel=no, and the temperature was just
around 3 to 5 K and never rose up. then I tried to give a velocities with
gen_temp though I don't know if it's correct or not.



2014-05-23 18:42 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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