[gmx-users] Using nose-Hoover thermostat with berendsen barostat
jpatil911 at gmail.com
Tue Jul 18 15:12:10 CEST 2017
Currently I am struggling with equilibrating the system. I am constraining a water molecule in a Bilayer at a fixed distance from the COM of the Bilayer. I tried many things like changing pressure coupling, temp coupling, varying time constants, rlist, varying step size, increasing warnangle, relaxing Lincs constrain, etc. But my system is blowing up after few nano seconds of simulation. Error is pressure coupling more than 1%. Volume was steady initially till few nano seconds and then suddenly it started oscillating and then system blows up. I checked every parameter one by one, varying in feasible range but no success. :(
The Bilayer I am using is simulated for 500ns. Bilayer properties are well estimated compared to experimental value. I am unable to get what I am doing wrong.
Any suggestion will be helpful.
> On 18-Jul-2017, at 5:37 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> The more Berendsen you use, the less physics you get ;-)
>> On Tue, 18 Jul 2017 13:44 jay patil <jpatil911 at gmail.com> wrote:
>> Hi Experts,
>> Can we use nose-Hoover thermostat in combination with berendsen barostat.
>> When I use grompp command, it gives warning berendsen will not give true
>> ensemble, and with -maxwarn 1 option I am able to run the simulation. My
>> doubt is: can we use this combination of thermostat and barostat. Or both
>> should be berendsen.
>> Any suggestion will be helpful.
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