<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks again, Justin.<br><br>Dear all,<br><br>I figured out the problem. Error was in my mdp file options. I did not specify the acc-groups correctly. I can get 1/viscosity using g_energy.<br><br>However, once the acc-groups are specified, now the NEW issue is not being able to run my job correctly.<br><br>I get the following errors:<br><br>Step 376, time 7.52 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.006964, max 0.163855 (between atoms 861 and 859)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br><br>----<br>-------<br><br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.5.4<br>Source code file: domdec.c, line: 4124<br><br>Fatal error:<br>A charge group moved too far between two domain decomposition
steps<br><br>---------------<br><br>I did not have any problems in my equilibrium simulations...this is happening in NEMD simulations.<br><br>Here is my .mdp file<br><br>title = Martini<br>cpp = /usr/bin/cpp<br>integrator = md<br>tinit = 0.0<br>dt = 0.01<br>nsteps =
500<br>nstcomm = 1<br>comm-grps = system<br>nstxout = 10<br>nstvout = 10<br>nstfout = 10<br>nstlog = 10<br>nstenergy =
10<br>nstxtcout = 2500<br>xtc_precision = 100<br>xtc-grps = <br>energygrps = system<br>nstlist = 1<br>ns_type = grid<br>pbc = xyz<br>rlist =
1.7<br>coulombtype = Shift <br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift <br>rvdw_switch = 0.9<br>rvdw = 1.2<br>DispCorr =
EnerPres<br>tcoupl = V-rescale<br>tc-grps = NGL W<br>tau_t = 1.0 1.0 <br>ref_t = 300. 300.<br>Pcoupl = No<br>Pcoupltype = Isotropic<br>tau_p = 1.0 <br>compressibility =
1e-5<br>ref_p = 1.0 <br>gen_vel = Yes<br>gen_temp = 300<br>gen_seed = 473529<br>constraints = None<br>constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 1<br>lincs_warnangle = 30<br><br>; Non-equilibrium MD
stuff<br>acc-grps = NGL W<br>accelerate = 0.1 0 0 -0.1 0 0<br>freezegrps = <br>freezedim = <br>cos_acceleration = 0.1 <br>deform = <br><br>Best,<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, 3:27 PM<br><br><div class="plainMail"><br><br>shikha nangia wrote:<br>> 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>> <br>>> /@Article{Hess2002b,<br>> />/ author = {B. Hess},<br>> />/ title = {Determining the shear viscosity of model liquids from />/molecular simulation},<br>> />/ journal = {J. Chem. Phys.},<br>> />/ year =
2002,<br>> />/ volume = 116,<br>> />/ pages = {209-217}<br>> />/}<br>> /<br>> <br>> 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>>> / Energy Average Err.Est. RMSD <br>> Tot-Drift<br>> />/ -------------------------------------------------------------------------------<br>> />/ 1/Viscosity / (/ s/kg)<br>> /<br>> <br>> <br><br>If the proper output options are not there, then there may have been a problem in the .mdp
file that prevented the correct energy terms from being written. If present in the .edr file, it should be shown in the list (sorry, I was thinking of something else). Please post your .mdp file.<br><br>-Justin<br><br>> Thanks again,<br>> <br>> SN<br>> <br>> --- On *Sat, 4/16/11, Justin A. Lemkul /<<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>>/* wrote:<br>> <br>> <br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> Subject: Re: [gmx-users] 1/viscosity from g_energy<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Saturday, April 16, 2011, 3:06 PM<br>>
<br>> <br>> <br>> shikha nangia wrote:<br>> > Dear gmx-users,<br>> ><br>> > I am trying to obtain 1/viscosity values for my system after<br>> using the cos_acceleration option in the mdp file. My gromacs<br>> 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>> > I am not sure which option (1 to 47) gives 1/viscosity. I tried<br>> looking through the manual and searching the user list but could not<br>> 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>> </mc/compose?to=<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<br>> <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 the www<br>>
interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> </mc/compose?to=<a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><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 the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"
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