Hi,
Thank you for replies.
>> 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.
In my case, the situation looks slightly different.
The pressure is not increasing at all (see xvg file in [1]), though it is only
500-ps simulation.
It is also averaged to the target pressure of 1.0.
For my case, the only problem is the constant drift of the conserved energy,
and everything others look at least reasonable to me.
> But if you are seeing constant drift, something is wrong.
Yes, it is constantly drifting. Is it better to file a report to redmine?
[1] https://www.dropbox.com/s/16bgfhvavqcw1f8/mttk05.xvg
On 2012年11月29日 02:07, Michael Shirts wrote:
Hi, all-
I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least
until 4.6.
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 <tarak20...@gmail.com> wrote:
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.s...@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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Postdoc @ Molecular Modeling & Simulation Group, Japan Atomic Energy Agency
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