Thanks again, Justin. Dear all,
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. However, once the acc-groups are specified, now the NEW issue is not being able to run my job correctly. I get the following errors: Step 376, time 7.52 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006964, max 0.163855 (between atoms 861 and 859) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length ---- ------- ------------------------------------------------------- Program mdrun, VERSION 4.5.4 Source code file: domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps --------------- I did not have any problems in my equilibrium simulations...this is happening in NEMD simulations. Here is my .mdp file title = Martini cpp = /usr/bin/cpp integrator = md tinit = 0.0 dt = 0.01 nsteps = 500 nstcomm = 1 comm-grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 2500 xtc_precision = 100 xtc-grps = energygrps = system nstlist = 1 ns_type = grid pbc = xyz rlist = 1.7 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = EnerPres tcoupl = V-rescale tc-grps = NGL W tau_t = 1.0 1.0 ref_t = 300. 300. Pcoupl = No Pcoupltype = Isotropic tau_p = 1.0 compressibility = 1e-5 ref_p = 1.0 gen_vel = Yes gen_temp = 300 gen_seed = 473529 constraints = None constraint_algorithm = Lincs unconstrained_start = no lincs_order = 1 lincs_warnangle = 30 ; Non-equilibrium MD stuff acc-grps = NGL W accelerate = 0.1 0 0 -0.1 0 0 freezegrps = freezedim = cos_acceleration = 0.1 deform = Best, SN --- On Sat, 4/16/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] 1/viscosity from g_energy To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Saturday, April 16, 2011, 3:27 PM shikha nangia wrote: > Thanks for your instant reply, Justin. > > Dear all, > > 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. > >> /@Article{Hess2002b, > />/ author = {B. Hess}, > />/ title = {Determining the shear viscosity of model liquids from > />/molecular simulation}, > />/ journal = {J. Chem. Phys.}, > />/ year = 2002, > />/ volume = 116, > />/ pages = {209-217} > />/} > / > > I am trying to get the results of viscosity through cos_acceleration that > probably are formatted as below (taken from a user-list). > >> / Energy Average Err.Est. RMSD > Tot-Drift > />/ > ------------------------------------------------------------------------------- > />/ 1/Viscosity / (/ s/kg) > / > > 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. -Justin > Thanks again, > > SN > > --- On *Sat, 4/16/11, Justin A. Lemkul /<jalem...@vt.edu>/* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] 1/viscosity from g_energy > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Saturday, April 16, 2011, 3:06 PM > > > > shikha nangia wrote: > > Dear gmx-users, > > > > 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. > > When I try using the g_energy option for my file > > > > g_energy -f ener.edr -o outfile.xvg > > > > I get the following options > > > > End your selection with an empty line or a zero. > > ------------------------------------------------------------------- > > 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 > > > 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. > > > > Please let me know what am I missing here. > > > > Use -vis rather than -o. > > -Justin > > > Thanks, > > SN > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > </mc/compose?to=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 > </mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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