vferra...@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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========================================
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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