Thanks for the tips. I just realized that there two other outputs two the g_energy -vis: evisco.xvg and eviscoi.xvg These files contain 5 columns among which the first one looks to be time. But what are the other 4? What are their differences? Regards,
Paymon -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 2:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation_2 On 2010-09-29 22.00, Payman Pirzadeh wrote: > Adding to my previous comments, It looks like that the third column is the > appropriate one to plot. However, I tried to use g_energy -b 0 -e 20000 to > take the whole trajectory (20000 ps) rather than half of the frames. But, > still g_energy take half of the frames. This has caused improper convergence > in viscosity values. If I take only the last 3000 ps (out of 10000ps), I > will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy > switches? > I think this is because it use an autocorrelation function of the pressure. By default it uses an FFT to compute it. The ACF at 20000 ps has very poor statistics (1 data point) and can therefore ruin the viscosity. Therefore ACFs by default are plotted to half the traj. There is a flag to get a longer (noisier) ACF. g_energy -h might tell you which one. > Payman > > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: September 29, 2010 1:03 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] viscosity calculation > > On 2010-09-29 20.52, Payman Pirzadeh wrote: >> Well, two questions: >> >> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks > like >> very weird to me since experimental value for water viscosity is 0.854 cP. >> My system is at 265K with 4202 molecules. Is sth strange going on? Or I am >> missing some unit conversions in the plot. >> > Is the experimental value 0.854 at that temperature? > Could be the the unit is different in the output too. Doesn't it say in > the xvg file? > >> 2. For calculation of protein diffusion constant, should we use the bulk > or >> shear viscosity of the solvent (water)? > Why not use g_msd? > >> >> Payman >> >> -----Original Message----- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Justin A. Lemkul >> Sent: September 29, 2010 12:28 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] viscosity calculation >> >> >> >> Payman Pirzadeh wrote: >>> Hello, >>> >>> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity >>> of my system which is water. Two files are generate: *.xvg and the >>> enecorr.xvg. Now, what should I do to calculate the viscosity of my >>> system with these two files? Sorry for such naïve question. >>> >> >> Plot the output .xvg; you will find it should contain two quantities: bulk >> and >> shear viscosity. >> >> -Justin >> >>> >>> >>> Regards, >>> >>> >>> >>> Payman >>> >>> >>> >>> >>> >> > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
