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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear GROMACS users,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I want to simulate a system consisting of a plate modeled by
atoms (5000 atoms) and a polyethylene chain (80 carbons). The plate is frozen
and I am using tabulated potentials. In this system, the considered interactions
are chain-chain and chain-plate. There are no electrostatic interactions. The
system is placed in a box, with dimensions corresponding to the dimensions of
plate and substantially larger height. My md.mdp file is as follows<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>cpp
= cpp<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>define
=<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>integrator
= md<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>dt
= 0.002<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nsteps
= 7500<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>nstcomm
= 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>comm_mode
= None<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>nstxout
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstvout
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstfout
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstxtcout
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstlog
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstenergy
= 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>energygrps
= Chain Plate<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>freezegrps
= Plate<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>freezedim
= Y Y Y<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>energygrp_excl = Plate
Plate<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>energygrp_table = Chain Chain
Chain Plate<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>nstlist
= 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>ns_type
= simple<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>rlist
= 0.4<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>pbc
= xyz<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>vdw-type
= User<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>rvdw
= 0.4<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>coulombtype
= cut-off<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>rcoulomb
= 0.1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Tcoupl
= nose-hoover<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>tc-grps
= System<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>tau_t
= 0.1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>ref_t
= 450<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=FR style='font-size:10.0pt;
font-family:Arial'>gen_vel
= yes<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>gen_temp
= 450<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>constraints
= none<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>pcoupl
= no<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>After launching this job the process is running but there is
no trajectory to be produced. The log file finishes in the section containing
following information<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> energygrp_flags[ 0]: 2 2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> energygrp_flags[ 1]: 2 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I have tried also running this job without user specified
potential, with relaxed plate, with pbc=no and some other attempts, but I always
failed in the same way. I would be very thankful for suggestions how to cope
with this problem. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Greetings<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Zuzana<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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