[gmx-users] several problems!!

[Lars Schaefer]

Hi Luca,


> 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?  
No, that's fine. Your structure should be sufficiently minimized then.

> 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?
the mdp-option is constraints = none
But why do you want to remove all the constraints for an AFM simulation? 
  What do you mean by "the molecule must to be uncostrained"? 
Constraints  basically act on the chemical bonds in your system to 
remove the fastest degrees of freedom and thus allow for a somewhat 
larger timestep of, say, 2fs. If you remove all constraints, you have to 
apply a smaller dt.

Cheers, Lars

> 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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-- 
*******************************************************
Lars Schäfer
MPI for biophysical Chemistry
Theoretical and computational Biophysics group
Department 070
Am Fassberg 11, D-37077 Goettingen
Tel: 0049 551 201-2305, Fax: 0049 551 201-2302
E-Mail: Lars.Schaefer at mpi-bpc.mpg.de
Home: http://wwwuser.gwdg.de/~lschaef2/homepage.html
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