I've just tried with a single CHCL3 molecule, here's the output:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1
Step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#
Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
Tolerance (Fmax) = 2.50000e+00
Number of steps = 100000
Step= 0, Dmax= 1.0e-02 nm, Epot= 0.00000e+00 Fmax= 0.00000e+00, atom= 0
writing lowest energy coordinates.
Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#
Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy = 0.0000000e+00
Maximum force = 0.0000000e+00 on atom 0
Norm of force = 0.0000000e+00
NOTE: 7 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists
in Your Family?" (Gogol Bordello)
The minimum is reached without steps, so... I don't know if the single
atom minimization wors or not...
Valerio
"Justin A. Lemkul" <[email protected]> ha scritto:
[email protected] 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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