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
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = cut-off
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?
Please help me, thank you in advance.
Valerio
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