Hi!
I had the same problem and this is what worked for me:
1. You must do an equilibration run WITHOUT any constraints (replace
constrained bonds with harmonic bonds (equilibrium bond length = constraint
length and force constant suitably high) and increase weight of H atoms to 10.0.
2. Do an equilibration run ( 1ns if practical) with this system.
3. Use the confout.gro file it generates to start your run WITH constraints
and the canonical H atom weights.
This should work.
Ashwin
________________________________
From: Ernesto Andres Román <indi...@hotmail.com>
To: gmx-users@gromacs.org
Sent: Thursday, 28 May, 2009 1:10:54 PM
Subject: [gmx-users] LINCS warnings (6153)
Dear gmx-user,
Im just making my first moves in protein dynamics
simulation. Ive done some tutorials and peptide-water simulations. But now im
intending to change the solvent to CCL4. Ive got the solvent parameters, made
the topology file, and the .gro file with the solvent and peptide together.
When I run mdrun commando an error message displays:
Fatal error:
Too many LINCS warnings (6153)
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 .mdp file is:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
Do you know what could be happening, and more important, how to solve it or
where to look for the problem ?
Thanks,
Ernesto.
________________________________
check out the rest of the Windows Live™.
More than mail–Windows Live™ goes way beyond your inbox. More than messages
Cricket on your mind? Visit the ultimate cricket website. Enter
http://beta.cricket.yahoo.com_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
