Re: [gmx-users] Diffusion coefficient water

The following paper may also be interesting. "System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016); http://dx.doi.org/10.1063/1.4960776

Re: [gmx-users] Diffusion coefficient water

See the following paper (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of diffusion calculations in GROMACS. The finite size correction for diffusion coefficients is something different than the long range energy corrections. A discussion of this (I can't vouch for all the

Re: [gmx-users] Diffusion coefficient water

Hi, I would also consider using a pressure-coupling algorithm that isn't known to create the wrong velocity distribution. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Diffusion coefficient water

Date: Wed, 17 Aug 2016 21:49:45 +0530 From: Nikhil Maroli <scinik...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Diffusion coefficient water Message-ID:

Re: [gmx-users] Diffusion coefficient water

er (li he) > > >-- > >Message: 1 >Date: Wed, 17 Aug 2016 21:49:45 +0530 >From: Nikhil Maroli <scinik...@gmail.com> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: >

Re: [gmx-users] Diffusion coefficient water

4. you could even try NVT ensemble 2016-08-18 2:25 GMT+08:00 li he : > I think you could try following things to see if you could get 'better' > results > 1. use time step of 0.2 or even 0.1 fs > 2. try different tau-t and tau-p, e.g. use larger tau-t > 3. try

Re: [gmx-users] Diffusion coefficient water

I think you could try following things to see if you could get 'better' results 1. use time step of 0.2 or even 0.1 fs 2. try different tau-t and tau-p, e.g. use larger tau-t 3. try different p-coupling methods 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk>: >

Re: [gmx-users] Diffusion coefficient water

On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote: Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get

Re: [gmx-users] Diffusion coefficient water

I don't think we can reproduce the exact results in MD .The overall behaviour of the system will be same .so it's obvious -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Diffusion coefficient water

Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a