<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks for your instant reply, Justin.<br><br>Dear all,<br><br>Please correct me if I am woring here....but...reading through the user-list, I gathered that -vis option og g_energy oes not give good results and instead cos_accleration should be used from the following reference.<br><pre>><i>@Article{Hess2002b,<br></i>><i> author =          {B. Hess},<br></i>><i> title =          {Determining the shear viscosity of model liquids from <br></i>><i>molecular simulation},<br></i>><i> journal =          {J. Chem. Phys.},<br></i>><i> year =          2002,<br></i>><i> volume =         116,<br></i>><i> pages =         {209-217}<br></i>><i>}<br></i></pre>I am trying to get the results of viscosity through cos_acceleration that probably are formatted as below (taken from a user-list). <br><br><pre>><i> Energy Average Err.Est. RMSD
Tot-Drift<br></i>><i> -------------------------------------------------------------------------------<br></i>><i> 1/Viscosity </i> (<i> s/kg)<br></i></pre><br>Thanks again,<br><br>SN<br><br>--- On <b>Sat, 4/16/11, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] 1/viscosity from g_energy<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Saturday, April 16, 2011, 3:06 PM<br><br><div class="plainMail"><br><br>shikha nangia wrote:<br>> Dear gmx-users,<br>> <br>> I am trying to obtain 1/viscosity values for my system after using the cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released on March 21, 2011. <br>> When I try using the g_energy option for my
file<br>> <br>> g_energy -f ener.edr -o outfile.xvg<br>> <br>> I get the following options<br>> <br>> End your selection with an empty line or a zero.<br>> -------------------------------------------------------------------<br>> 1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR) 5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En. 9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC 13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ
17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume 21 Density 22 pV 23 Enthalpy 24 Vir-XX 25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36
Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47 Lamb-System <br>> <br>> I am not sure which option (1 to 47) gives 1/viscosity. I tried looking through the manual and searching the user list but could not resolve the issue.<br>> <br>> Please let me know what am I missing here.<br>> <br><br>Use -vis rather than -o.<br><br>-Justin<br><br>> Thanks,<br>> SN<br>> <br>> <br><br>--
========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use
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