Re: [ESPResSo-users] NPT simulations

[Ulf Schiller]

Raffaela,

It's been a while (i.e. several years) since I looked into the NPT 
integrator, but let me try to answer your questions.

On 02/15/2017 10:22 AM, Raffaela Cabriolu wrote:
> I have then implemented a script with those lines:
>
> integrate set npt_isotropic /p_ext piston_mass/
> thermostat npt_isotropic /temperature gamma0 gammaV/
> thermostat langevin /temperature gamma/

I am not sure whether the 'langevin' and 'npt_isotropic' thermostat are 
compatible. I believe the NPT integrator has its own Langevin thermostat 
built in, so switching both of them on at the same time may lead to 
undesirable/unphysical effects. This should be fairly straightforward to 
validate by checking the measured temperature and diffusion in the system.

> To understand how to set the friction factors and the piston mass I am
> referring to the paper by Kolb and Dunweg J.Chem. Phys.,
> 111(10):4453–59, 1999.
> It is not clear to me the meaning of the friction factors in the command
> above.
> According to the paper by Kolb and Dunweg there are two damping
> parameters. The damping γ0 in the paper is related to the particle
> relaxation time while γV is related to the volume relaxation time. Are
> those two factors in the paper coinciding, respectively, with /gamma0/
> and /gammaV/ of the NPT isotropic protocol described by the command line
> above ?
>
> My doubts comes from the fact that I have found a link where the value
> of the parameters /piston_mass, gamma0 and gammaV/ are discussed for
> espressoMD NPT protocoll:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__espressomd.org_html_despresso-5Fmails.html&d=DwIDaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=vo_59UgGQLPOFUG9XRo42qkxDB-wQV2VznPwVSffS30&m=vlLM8ZyGTB4zHzfw0lDj1rvA_JLNVThm6sXx2FuSouo&s=qGgxEhaAsJlixqWubiG9I0q94JPVIuV7ArKd0pS8ftI&e= 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__espressomd.org_html_despresso-5Fmails.html&d=DwMFAw&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=MAz9adTwp8sb65WmGjE0_2cwq2jbeMCasgNuNhEb7Gk&m=lzdEWvnDyg296gK_W8nWKvDTupJDrNy1YBGHGWndjPA&s=nTu8i3smkkQd3GZhFYYtZtuSnBu6ac9HlNdPvKHvAf4&e=>
> In the link those value are given as:
> setmd piston 0.0001
> setmd g0 0.001
> setmd gv 0.5
>
> But g0 assumes the optimal value of γV in the paper, while gv assumes
> the optimal value of γ0 in the paper.

I think your doubts are absolutely justified. Looking at the script 
"npt.tcl" in the testsuite, I suspect that the parameters in the link 
you found are inverted. I would start with the values given in the paper 
and check if you can reproduce the dampening of the transient oscillations.

> Furthermore, I would like to understand better the role of the
> "Langevin" command line. The temperature in "thermostat npt_isotropic"
> should be the same as in "thermostat langevin" command ? Gamma should
> not be equal to the the friction term for the particles velocities, then
> coinciding with gamma0 ?

As I said above, using both 'npt_isotropic' and 'langevin' may lead to 
double dampening of the velocities which would change the diffusion 
coefficient. So be sure to carefully check that you get correct behavior.

Hope this helps.

Thanks,
Ulf

--
Dr. Ulf D. Schiller
Assistant Professor, Department of Materials Science and Engineering
Faculty Scholar, School of Health Research
Clemson University
161 Sirrine Hall
Clemson, SC 29634

Office: 299c Sirrine Hall
Phone: 1-864-656-2669
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