sure, here it is :<br>**************************************<br>; 50ns NVT production<br>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 = 50000 ; every 100 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>; 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<br>*******************************************<br>
<br><br><br><div class="gmail_quote">On Wed, Nov 5, 2008 at 4:22 PM, Ángel Piñeiro <span dir="ltr"><<a href="mailto:angel.pineiro@usc.es">angel.pineiro@usc.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="ES-MX">
<div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="EN-US">Are you working at constant volume? It would be useful to see
your mdp file…</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="EN-US"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="EN-US">Angel.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="EN-US"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);" lang="EN-US"> </span></p>
<div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p><b><span style="font-size: 10pt;" lang="ES">De:</span></b><span style="font-size: 10pt;" lang="ES">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>En
nombre de </b>xianghong qi<br>
<b>Enviado el:</b> miércoles, 05 de noviembre de 2008 10:18 p.m.<br>
<b>Para:</b> Discussion list for GROMACS users<br>
<b>Asunto:</b> [gmx-users] Re: density vs time?</span></p>
</div><div><div></div><div class="Wj3C7c">
<p> </p>
<p>Hello, all:<br>
<br>
I checked the mailing list. Looks like g_energy can calculate density vs time,
but <br>
my g_energy doesn't have options like density, volume? I am wondering how
I can<br>
get my density vs time graph? Any suggestion is appreciated. Thanks. <br>
<br>
-Xianghong Qi<br>
<br>
<br clear="all">
<br>
-- <br>
Some people make the world more special just by being in it.</p>
</div></div></div>
</div>
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