<div>Hi, Mark, </div>
<div><br>I use the command: grompp -f md.mdp -c eq2.gro -p conf.top -n md.ndx -o md.tpr -t eq2.trr</div>
<div>and index file was makde from command make_ndx, I named the two methanes as methane1 and methane2.</div>
<div>and my mdp file is : </div>
<div> </div>
<div>integrator = sd<br>ld_seed = -1<br>; start time and timestep in ps<br>tinit = 0<br>dt = 0.002<br>nsteps = 25000000<br>; number of steps for center of mass motion removal =<br>
nstcomm = 100<br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f) =<br>nstxout = 25000000<br>nstvout = 25000000<br>nstfout = 0<br>
; Output frequency for energies to log file and energy file<br>nstlog = 500 ; every 1 ps<br>nstenergy = 50000 ; every 100 ps<br>; Output frequency and precision for xtc file<br>nstxtcout = 50 ; every 0.1 ps<br>
xtc-precision = 10000<br>xtc_grps = system<br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency =<br>nstlist = 10<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>
; Periodic boundary conditions: xyz or none<br>pbc = xyz<br>; nblist cut-off<br>rlist = 1.0<br>domain-decomposition = no<br>; Turn off intermolecular interaction between CH4:</div>
<div>energygrp_excl = Methane1 Methane2<br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = pme<br>;rcoulomb-switch = 0<br>rcoulomb = 1.0<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = switch<br>; cut-off lengths<br>rvdw = 0.9<br>
rvdw-switch = 0.8<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; OPTIONS FOR TEMPERATURE COUPLING<br>tc_grps = system<br>tau_t = 1.0 ; Langevin friction constant (ps)<br>
ref_t = 300<br>;OPTIONS FOR PRESSURE COUPLING<br>Pcoupl = No<br>pcoupltype = isotropic<br>tau_p = 5.0<br>compressibility = 4.5e-05<br>ref_p = 1.0<br>
; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br>; OPTIONS FOR BONDS<br>constraints = hbonds<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>; Do not constrain the start configuration<br>
unconstrained-start = yes</div>
<div>*******************************************************</div>
<div>I can't understand why Methane1 is not an energy group. </div>
<div>Thanks for your help. </div>
<div>-Xianghong Qi</div>
<div> </div>
<div> </div>
<div><br><br> </div>
<div class="gmail_quote">On Wed, Nov 19, 2008 at 3:04 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">xianghong qi wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi, Mark:<br> I made the index file and call two methanes as methane1 and methane2 , then I set energygrp_excl = methane1 methane2, but when I run grompp, it said methane1 is not an energy group. What do you understand this problem? Thanks. -Xianghong Qi<br>
</blockquote><br></div>You haven't done what you think you've done. I can't tell what you've done wrong because you haven't told me what you've done, i.e. examples and command lines. My guess is that you didn't supply your index file to grompp, so it can't tell what the definition is.
<div>
<div></div>
<div class="Wj3C7c"><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Some people make the world more special just by being in it.<br>