[gmx-users] nve energy conservation
jojo412202 at gmail.com
Fri Mar 16 19:42:30 CET 2018
Thank you for your reply!
I am attempting to conserve energy in an NVE run of 1000 SPCE water - I
have tried a number of different verlet-buffer-tolerances (0.001 to 5e-5),
sometimes the run output file suggests a specific verlet buffer-tolerance.
However I am still experiencing ~600 kJ/mol shift per ns. I have tried
double precision which does not seem to make a difference. I also use a
potential modifier (potential-shift) to ensure the potential reaches 0. I
have tried turning off the charges (to see if the ewald parameters are the
source of the problem), but the same massive energy shift occurs - which
leads me to believe the ewald parameters are not the source of the problem.
I am using 'settle' to constrain the water molecule. I am suspicious that
this could be the cause of the energy shift. Although, looking at some of
the previous posts on gromacs email forums, it appears that 'settle' has
not been a problem for energy conservation previously.
I have also tried different versions of Gromacs (5.1.4 and 2018), but the
energy shift still occurs.
Can you recommend any other parameters to change? Or any other strategies
to go about conserving energy for NVE?
On Wed, Mar 14, 2018 at 5:16 PM, Mark Abraham <mark.j.abraham at gmail.com>
> That setup is guaranteed to leak. You specified -1 for the tolerance which
> means you get to control rlist to choose the buffer size, which is zero
> because you chose it to match both rcoulomb and rvdw. Check out the docs of
> verlet-buffer-tolerance and try something else!
> On Wed, Mar 14, 2018, 20:08 Jo <jojo412202 at gmail.com> wrote:
> > Hello,
> > I posted earlier regarding running an NVE simulation for a box of 1000
> > water. I have tried many different parameters based on other gmx_users
> > email list questions (changing verlet-buffer-tolerance, timesteps,
> > coulombtype, vdw-type, etc), but still I am unable to conserve energy.
> > energy shift is catastropic (~300 kJ/mol/ns).
> > Thanks Mark for referring me earlier to the manual with the energy drift
> > figure! I think the drift I am experiencing is much more significant
> > that depicted in the figure though.
> > Below are the parameters I am using, I feel like I must be making a major
> > mistake in my mdp file. I assume using Potential-shift for coulombic and
> > vdw will satisfy energy conservation for both energies. I have not tried
> > double precision yet but I assume it will not help with the massive
> > shift I am seeing.
> > Please let me know if anyone has any suggestions on what I can try or
> > anything I am wrongly assuming!
> > verlet-buffer-tolerance = -1
> > rlist = 1.3
> > coulombtype = PME
> > rcoulomb = 1.3
> > coulomb-modifier = Potential-shift
> > vdw-type = Cut-off
> > rvdw = 1.3
> > vdw-modifier = Potential-shift
> > Best,
> > Jo
> > --
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