[gmx-users] several problems!!

luca deriu lucaderiu77 at yahoo.it
Mon Oct 18 14:55:44 CEST 2004

I'm a new gromacs user. I try to perform a
equilibration mdrun of a sistem composed by 2 spectrin
repeats (211 residues) and 360000 SPC216 water
molecules.I perfomed a energy minimization of the
protein first in vacuum after in water.I heat the
sistem at 300K.Now I'm trying to do a long mdrun (1ns)
to equilibrate the sistem.I've got several
problems.I'm working with gromacs 3.2.1 in single
precision.I don't know how to work in double
1)When I performed the e.m.the message 'converged with
machine precision but did not reach the request
force'appears.Is it a problem?  
2)When I try to do the equilibration mdrun appears
that a 'water molecule can not to be settled'.I try to
reduce time step but it is the same thing.I restart
the run where it finished with tpbconv.I'm doing the
right thing?
3)I don't want use constraint because I'll want
perform a AFM and I know that the molecule must to be
uncostrained.I set constraint = none, but I've seen
that in the run input file there is constraint
algorythm = LINCS. My sistem is constrained or
This is my parameter files:
title               =  
cpp                 = /lib/cpp
define              =  
integrator          = md
dt                  = 0.002  
nsteps              = 500000; 1000 ps!
nstxout             = 1000
nstvout             = 1000
nstlog              = 1000
nstenergy           = 100
nstxtcout           = 2000
xtc_grps            = Protein
energygrps          = Protein  SOL 
rlist               = 1.0
rcoulomb            = 1.0
rvdw                = 1.0
tcoupl              = Berendsen
tc-grps             = Protein   SOL  SO4
tau_t               = 0.1 0.1 0.1
ref_t               = 300 300 300
gen-vel             = yes
gen-temp            = 300
gen-seed            = 173529

Thanks a lot in advance for any help and excuse me for
the bad English and the long mail.    

Luca Deriu,
Politecnico di Milano.
lucaderiu77 at yahoo.it

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