[gmx-users] Question about conserved energy in MTTK

[tarak karmakar]

Hi,

I was also facing the same problem. If you check your pressure during
this NPT run, u can see that it got increased to a higher value. I had
posted the same problem few days back, u can follow the thread. It
seems MTTK is not stable enough and is not performing well in this
context. So I have moved to Leap-frog, Nose-Hoover, Parinello-Rahman
combination for the NPT simulation. There is one paper as well by
Prof. Shirts in JCTC.

Cheers,
Tarak

On Thu, Nov 22, 2012 at 2:08 PM, Shun Sakuraba <sakuraba.shun at jaea.go.jp> wrote:
> Dear list,
>
> I am trying to use MTTK barostat in GROMACS 4.5.5.
> After analyzing the result for a while, I found that the conserved energy (not total energy) of MTTK is drifting during the simulation.
> The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a constant ratio of ca. -185 kJ/mol/ps.
>
> I cannot believe this is an expected behavior, so could anyone point out where I am wrong in my simulation setup? I found similar report at [3] but seems it was when 4.5 was in pre-release stage.
>
> Thanks in advance for your help!
>
> * Simulation detail
> The system consists of 1000 SPC-E water molecules, and the time step is set to 0.5 fs, just in case the long timestep harms the conserevation (c.f. [3]). The interaction energy is set to switching version, just in case, too. Changing these parameter does not seem to improve the conservation.
> The double precision version of GROMACS is used (single precision version also has the same problem).
> The system has been pre-equilibrated with Berendsen pressure coupling simulation with the same pressure and temperature.
>
> [1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg
> [2] https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr
> [3] http://lists.gromacs.org/pipermail/gmx-developers/2010-January/003979.html
>
> == .mdp file contents follow
>
> integrator = md-vv
> define =
>
> dt = 0.0005
> nsteps = 1000000 ; 500 ps
>
> coulombtype = PME-Switch
> vdwtype = Switch
> pbc = xyz
>
> rlist = 1.2
> rcoulomb = 1.0
> rcoulomb_switch = 0.9
> rvdw = 1.0
> rvdw_switch = 0.9
> nstlist = 1
>
> tinit = 0
> tcoupl = nose-hoover
> tc_grps = System
> tau_t = 0.5
> ref_t = 300.0
> nsttcouple = 1
>
> pcoupl = MTTK
> pcoupltype = isotropic
> compressibility = 4.5e-5
> ref_p = 1.01325
> tau_p = 0.5
> refcoord_scaling = no
> nstpcouple = 1
>
> constraints = hbonds
> constraint_algorithm = LINCS
>
> nstxtcout = 100
> nstlog = 100
> nstenergy = 100
> nstvout = 0
> nstxout = 1000
>
> --
> Shun SAKURABA, Ph.D.
> Postdoc @ Molecular Modeling & Simulation Group, Japan Atomic Energy Agency
> --
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