[gmx-users] Question about conserved energy in MTTK
mrshirts at gmail.com
Wed Nov 28 18:07:03 CET 2012
I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least
A random-walk drift in the conserved energy is actually what MTTK
gives -- it's not as conserved as, say, energy conservation, it just
has an expectation value of zero drift over time, which means that the
RMSD will increase with time according to sqrt(dt).
But if you are seeing constant drift, something is wrong.
On Wed, Nov 28, 2012 at 7:20 AM, tarak karmakar <tarak20489 at gmail.com> wrote:
> 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.
> 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  and . 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  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. ). 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.
>>  https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg
>>  https://www.dropbox.com/s/tg8butw39rmz8qk/mttk05.edr
>>  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
>> gmx-users mailing list gmx-users at gromacs.org
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