<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
<pre>Dear all;<br><br>I ran a simulation using two tabulated potentials for two energy groups but it seems that <br>Gromacs is not generating any potential because LJ energies = 0.0000 in every step.<br><br>The groups are TET and HS and they are represented in index.ndx. Their tabulated potentials<br>are table_TET_TET.xvg and table_HS_HS.xvg respectively. The charge of every atom is zero and<br>the Gromacs version is 3.3.3.<br><br>My parameter and md.log files are:<br><br>#################### Parameter file ########################### <br>integrator = sd<br>dt = 0.001<br>nsteps = 100000<br>nstxout = 100<br>nstvout = 100<br>nstfout = 100<br>nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 100<br>xtc_grps = System<br>energygrps = TET HS<br>energygrp_table = TET TET HS HS<br>energygrp_excl = TET HS<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br><br>coulombtype = User<br>rcoulomb = 1.0<br>epsilon_rf = 80<br><br>vdwtype = User<br>rvdw = 1.0<br><br>tcoupl = Berendsen<br>tc-grps = System<br>tau_t = 0.2<br>ref_t = 300<br><br>Pcoupl = no<br>tau_p = 1.0<br>compressibility = 4.46e-5<br>ref_p = 1.0<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed =-1<br> ###############################################################<br><br> tables: table_TET_TET.xvg & table_HS_HS.xvg<br><br><br>>mdrun_mpi -s topol.tpr -table table.xvg -x traj -o traj -g md<br><br><br>########################## md.log file ##########################<br>.<br>.<br>.<br>Table routines are used for coulomb: TRUE<br>Table routines are used for vdw: TRUE<br>Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br>System total charge: 0.000<br>Read user tables from table_TET_TET.xvg with 12582 data points.<br>Tabscale = 4838.85 points/nm<br>Read user tables from table_HS_HS.xvg with 12402 data points.<br>Tabscale = 4769.62 points/nm<br>.<br>.<br>.<br><br> Step Time Lambda<br> 23000 23.00000 0.00000<br> Energies (kJ/mol)<br> Bond Angle LJ (SR) Coulomb (SR) Potential<br> 4.79413e+03 2.18701e+03 0.00000e+00 0.00000e+00 6.98115e+03<br> Kinetic En. Total Energy Temperature Pressure (bar)<br> 1.36561e+04 2.06372e+04 3.04239e+02 7.13050e+01<br>.<br>.<br>. <==== A V E R A G E S ====><br> <== ############### ======><br>.......<br><br> Epot (kJ/mol) Coul-SR LJ-SR <br> TET-TET 0.00000e+00 0.00000e+00<br> TET-HS 0.00000e+00 0.00000e+00<br> HS-HS 0.00000e+00 0.00000e+00<br>.<br>.<br>.<br>##############################################################<br><br><br>Could you please tell me what is wrong ?<br><br><br>P.S.<br><br>even I have tried:<br><br>mdrun_mpi -s topol.tpr -table table.xvg -tablep table_TET_TET.xvg table_HS_HS.xvg <br>-x traj -o traj -g md<br><br>But I got the same result.<br><br><br>Thanks in advance,<br><br>Harry G.<br></pre><br /><hr />Insert movie times and more without leaving HotmailŪ. <a href='http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd1_052009' target='_new'>See how.</a></body>
</html>