[gmx-users] links warnangles

[Justin A. Lemkul]

vferrario at units.it wrote:
> Dear all,
> I'm dealing with a simulation of a polymer in CHCL3, the polymer works 
> good, but I have some problems with the CHCL3 definition in GROMOS 53a6 ff.
> I've taken the CHCL3 definition from the automated topology builder 
> website:
> 
> http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom
> 
> So the itp file of my CHCL3 definition is:
> 
> [ moleculetype ]
> ; Name            nrexcl
> CLF             3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1        CCL      1    CLF    CCl      1      0.179     12.011   ; 
> qtot 0.179
>      2        HCL      1    CLF    HCl      1      0.082      1.008   ; 
> qtot 0.261
>      3       CLCL      1    CLF    CL1      1     -0.087     35.453   ; 
> qtot 0.174
>      4       CLCL      1    CLF    CL2      1     -0.087     35.453   ; 
> qtot 0.087
>      5       CLCL      1    CLF    CL3      1     -0.087     35.453   ; 
> qtot 0
> 
> [ constraints ]
>     1     3     1     0.1758
>     1     4     1     0.1758
>     1     5     1     0.1758
>     2     3     1     0.233839
>     2     4     1     0.233839
>     2     5     1     0.233839
>     3     4     1     0.290283
>     3     5     1     0.290283
>     4     5     1     0.290283
> 
> I've generated a box of solvent, but when I try to minimize it with the 
> following mdp file:
> 
> title                = Minimization
> cpp                = /lib/cpp
> include                = -I../top
> constraints             = none
> integrator            = steep
> emtol                = 2.5
> emstep                  = 0.01
> nsteps                = 100000
> nbfgscorr               = 10
> nstenergy            = 100
> nstxtcout            = 0
> xtc_grps            = system
> energygrps            = system
> nstlist                = 5

For EM, nstlist should be 1.

> ns_type                = grid
> pbc                     = xyz
> rlist                = 1.0
> coulombtype            = cut-off

Plain cutoffs lead to bad artifacts and thus should generally not be used.

> rcoulomb            = 1.0
> vdwtype                 = cut-off
> rvdw                = 1.4
> fourierspacing            = 0.15
> fourier_nx              = 0
> fourier_ny              = 0
> fourier_nz              = 0
> pme_order               = 4
> optimize_fft            = yes
> tcoupl                  = no
> pcoupl                  = no
> gen_vel                 = no
> constraint_algorithm    = LINCS
> lincs_order             = 8
> lincs_iter              = 2
> nstlog                  = 100
> lincs_warnangle         = 90
> 
> The system crash giving me the following error:
> 
> Fatal error:
> Too many LINCS warnings (1413)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> 
> My question is: why the system crash and why LINCS warnings are 
> generated if all the molecule is constrained? What shell I do to avoid 
> these probles? New CHCL3 definition?

The charges and atom types match exactly what the force field prescribes, so 
those are probably solid.

You need to simplify the problem.  You built a box, but it is failing.  Does an 
EM of a single molecule work, or does it fail as well?  Consult the following:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

> Please help me, thank you in advance.
> 
> Valerio
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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