[gmx-users] running a simulation without production

[Zuzana Benkova]

  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Zuzana Benkova
Sent: Monday, November 03, 2008 5:49 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] running a simulation without production

 

Dear GROMACS users,

 

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

 

cpp                 =  cpp

define              =

 

integrator          =  md

dt                  =  0.002

nsteps              =  7500

nstcomm             =  1

comm_mode           =  None

nstxout             =  10

nstvout             =  10

nstfout             =  10

nstxtcout           =  10

nstlog              =  10

nstenergy           =  10

energygrps          =  Chain Plate

freezegrps          =  Plate

freezedim           =  Y Y Y

energygrp_excl      =  Plate Plate

energygrp_table     =  Chain Chain Chain Plate

nstlist             =  1

ns_type             =  simple

rlist               =  0.4

pbc                 =  xyz

vdw-type            =  User

rvdw                =  0.4

coulombtype         =  cut-off

rcoulomb            =  0.1

Tcoupl              =  nose-hoover

tc-grps             =  System

tau_t               =  0.1

ref_t               =  450

gen_vel             =  yes

gen_temp            =  450

constraints         =  none

pcoupl              =  no

 

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

 

   energygrp_flags[  0]: 2 2

   energygrp_flags[  1]: 2 1

 

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. 

 

Greetings

 

Zuzana

 

 

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