Re: [gmx-users] Annealing of shell polarizable water model

2011-03-23 Thread Ivan Gladich
Dear Justin, Dear all you guessed right. I am now using a v-rescale thermostate and it works fine and it also runs in parallel. Here below the changed part in my grompp with the v-rescale thermostate. Thanks a lot Ivan ### ;OPTIONS FOR ANNELING annealing

Re: [gmx-users] Annealing of shell polarizable water model

2011-03-22 Thread Justin A. Lemkul
Ivan Gladich wrote: Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still short (due by the serial run), the temperature profiles are the same (see attached file). As further check, I removed the annealing and the temperature rises

Re: [gmx-users] Annealing of shell polarizable water model

2011-03-22 Thread Ivan Gladich
Dear David Dear all I did the serial run with the same topology and grompp: even if the simulation time is still short (due by the serial run), the temperature profiles are the same (see attached file). As further check, I removed the annealing and the temperature rises to 160 K after ~0.5ps

Re: [gmx-users] Annealing of shell polarizable water model

2011-03-22 Thread Ivan Gladich
Yes, I am running in parallel... Now I will try to run in serial to see if the problem persist Thanks Ivan On 03/22/2011 10:00 AM, David van der Spoel wrote: On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of

Re: [gmx-users] Annealing of shell polarizable water model

2011-03-22 Thread David van der Spoel
On 2011-03-22 10.37, Ivan Gladich wrote: Dear all, I would like to heat, very slowly, a ice box of 1796 SWM4-NDP water. This kind of water has 4 sites plus a shell and I am using a small time step (0.1 fms) to heat my ice box from 0 K top 160K in 1 ns. To do that I used a linear annealing from 0