[gmx-users] several problems!!

[Maximiliano Figueroa]

You must equilibrate the system with water. First a E.M., then a short
MD when restrains, and then the full MD. If you don´t do that, the
full MD don´t work, and your system die (the 2) point that you tell in
your e-mail).

Max


On Mon, 18 Oct 2004 14:55:44 +0200 (CEST), luca deriu
<lucaderiu77 at yahoo.it> wrote:
> Hi,
> 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
> precision.
> 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
> uncostrained?
> 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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