Re: [gmx-users] ionic liquids - viscosity via green kubo relation
Hello, I would try to extend ACF window (10, 50, 200ps) but not too much since you might end with integrating noise which would lead to overestimation of viscosity. For water, 4ps seems to be ok but your liquid might have longer ACF tail so you are actually getting seriously underestimated viscosity. You should also run calculations for Pxz, Pyz, (Pxx-Pyy)/2 and (Pyy-Pzz)/2 to improve statistics. Regards, km. On Tue, May 7, 2013 at 4:13 PM, Thomas P tomas...@gmail.com wrote: Hello all, I have a periodic system of composed of 200 pairs of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. I equilibrate the system for 1.5 ns to the appropriate density under 1 atm and 300 K in the NPT ensemble. As a sidenote, I do obtain the density cited in the literature for the system and force field in question. Once equilibrated, I pass into the NVE ensemble, and store the the Pxy pressure tensor component of the entire group of atoms. I am doing this to calculate the viscosity of my liquid using the Green-Kubo relation. I have been calculating the Stress Autocorrelation Function (SACF) for Pxy using Matlab. The autocorrelation window is 4 ps, and data was stored over a 1 ns production run every 5 fs (200 000 data points). I know a 1 ns run may be slightly short for an ionic liquid, but the simulations take quite a long time already, and I therefore wanted to rule out any other issues before doing a longer run. The SACF (normalized to 1) that I obtain is attached, and I do not really know what to make of it; it is not smooth at all (quite jaggedy in fact!). Furthermore, when I integrate to compute the viscosity (I do not integrate the normalized curve obviously), I obtain around 6 cP which is 2 orders of magnitude too small... I am quite sure there are no errors in the parameters of my force field, maybe someone can suggest something that I may have missed? -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] On the usage of SD integrator as the thermostat
I am wondering what you mean by 'proper dynamics', Chris? And in general, what's the advantage of using sd integrator over md integrator together with Nose-Hoover thermostat. Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I use the SD integrator with tau_t = 1.0 ps for all of my work, including proteins in aqueous solution or embedded in a lipid membrane. Any value of tau-t is correct, and none will give you the proper dynamics, but I find that the diffusion of both water and lipids is quite reasonable when using tau_t=1.0 ps. I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest that you search out those old posts. Chris. -- original message -- In manual I've found possibility of the usage of the sd (langeven's dynamics) integrator as the thermostat. It's known that friction coefficient in the Langeven's equations is defined as m/Tau_t. So the high values of tau t can be appropriate for the modeling of the thermostat without t_coupl. Also I know that friction coefficient for such simulation must corresponds to the viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 ps can be appropriate value for such simulations. Does this value suitable for water-soluble system only ? What Tau_t should I use for modeling of the membrane proteins in the lipid-water environment which has higher viscosity ? Thanks for help, James -- gmx-users mailing listgmx-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 listgmx-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] customized pairtypes with OPLS/AA
Hi, I want to influence slightly the way VdW interactions are calculated by providing customized values of sigma/epsilon in [ pairtypes ]. I employ OPLS/AA. The section of my molecule definition looks like, say: [ pairtypes ] CT CT 1 0.33 0.2 When I run grompp I get the following error message: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 857 Fatal error: Atomtype CT not found What am I doing wrong? Overriding default definition of bondtypes, angletypes, or dihedraltypes works just fine. Regards, Krzysztof -- gmx-users mailing listgmx-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
Re: [gmx-users] customized pairtypes with OPLS/AA
Justin, Thank you very much. I assume that pairs in pairtypes are used to calculate 1-4 VdW interactions only and do not influence calculations of short range VdW? Regards, km. On Wed, Aug 29, 2012 at 6:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/29/12 11:37 AM, Krzysztof Murzyn wrote: Hi, I want to influence slightly the way VdW interactions are calculated by providing customized values of sigma/epsilon in [ pairtypes ]. I employ OPLS/AA. The section of my molecule definition looks like, say: [ pairtypes ] CT CT 1 0.33 0.2 When I run grompp I get the following error message: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 857 Fatal error: Atomtype CT not found What am I doing wrong? Overriding default definition of bondtypes, angletypes, or dihedraltypes works just fine. All of those are bonded terms and use atomtype names that are translated from their opls_* equivalents. In ffnonbonded.itp, you need to use opls_* atomtypes. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
