Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david
On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/12 11:46 AM, rama david wrote: > >> Thank you for your Help. >> >> I did the following tc-groups >> >> tcoupl = V-rescale ; modified Berendsen thermostat >> tc-grps = extra34 Non-Protein energy ; two coupling groups - >> more accurate >> tau_t = 0.1 0.1 0.1 ; time constant, in ps >> ref_t = 310 310 310 ; reference temperature, one for each >> group, in K >> ; >> >> Energy contain the residues that i needed >> extra34 contain all the remaining ligand and receptor atom >> non-protein contain sol and ion. >> >> I got the energy file after mdrun -rerun >> >> I used the g_energy term >> >> It give me the following output >> End your selection with an empty line or a zero. >> ------------------------------**------------------------------**------- >> 1 G96Angle 2 Proper-Dih. 3 Improper-Dih. 4 >> LJ-14 >> 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 >> Disper.-corr. >> 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 >> Kinetic-En. >> 13 Total-Energy 14 Temperature 15 Pres.-DC 16 >> Pressure >> 17 Constr.-rmsd 18 Box-X 19 Box-Y 20 >> Box-Z >> 21 Volume 22 Density 23 pV 24 >> Enthalpy >> 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 >> Vir-YX >> 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 >> Vir-ZY >> 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 >> Pres-XZ >> 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 >> Pres-ZX >> 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 >> Box-Vel-XX >> 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X 48 >> Mu-Y >> 49 Mu-Z 50 T-extra34 51 T-non-Protein 52 >> T-energy >> 53 Lamb-extra34 54 >> Lamb-non-Protein >> 55 Lamb-energy >> >> >> So I confused. though it shows the energy group, which option should i >> have >> to choose ?? >> >> What is Lamb-energy??? >> >> > It is related to temperature coupling. > > > Is I did any mistake??? or I have to use any else command ?? >> >> > I have told you to use "energygrps" (which is described in the manual) and > you're specifying "tc-grps." Temperature coupling and energy calculation > groups are very different concepts. > > > -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/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
