Hi guys,<br><br>As Justin pointed out, it was the problem with md simulation blowing up. I also had coloumbtype=PME and had to switch to cut-off to make my simulation run faster. <br><br>Thanks for all the help.<br><br><div class="gmail_quote">
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">jochen@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
<br>
delta_t = 0.01<br>
<br>
You are using a 10 fs timestep!!! That is way too long. Standard is 2 (with bond constraints).<br>
<br>
<br>
<br>
Yongchul Chung wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
Hi all,<br>
<br>
I am trying to simulate 100 molecules of n-alkane molecules but keep receiving LINC errors.<br>
When I completed steepest descent I received following msg:<br>
<br>
Steepest Descents converged to Fmax < 500 in 819 steps<br>
Potential Energy = 1.7174361e+05<br>
Maximum force = 4.4903098e+02 on atom 172<br>
Norm of force = 3.0003010e+01<br>
<br>
Then I performed mdrun with the output of this file and gets LINCS warning:<br>
<br>
<br>
Input Parameters:<br>
integrator = md<br>
nsteps = 8000<br>
init_step = 0<br>
ns_type = Grid<br>
nstlist = 10<br>
ndelta = 2<br>
nstcomm = 1<br>
comm_mode = Linear<br>
nstlog = 10<br>
nstxout = 250<br>
nstvout = 1000<br>
nstfout = 0<br>
nstenergy = 10<br>
nstxtcout = 0<br>
init_t = 0<br>
delta_t = 0.01<br>
xtcprec = 1000<br>
nkx = 125<br>
nky = 125<br>
nkz = 125<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 0<br>
epsilon_surface = 0<br>
optimize_fft = TRUE<br>
ePBC = xyz<br>
bPeriodicMols = FALSE<br>
bContinuation = FALSE<br>
bShakeSOR = FALSE<br>
etc = V-rescale<br>
epc = No<br>
epctype = Isotropic<br>
tau_p = 1<br>
ref_p (3x3):<br>
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress (3x3):<br>
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
refcoord_scaling = No<br>
posres_com (3):<br>
posres_com[0]= 0.00000e+00<br>
posres_com[1]= 0.00000e+00<br>
posres_com[2]= 0.00000e+00<br>
posres_comB (3):<br>
posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br>
posres_comB[2]= 0.00000e+00<br>
andersen_seed = 815131<br>
rlist = 1<br>
rtpi = 0.05<br>
coulombtype = PME<br>
rcoulomb_switch = 0<br>
rcoulomb = 1<br>
vdwtype = Cut-off<br>
rvdw_switch = 0<br>
rvdw = 2<br>
epsilon_r = 1<br>
epsilon_rf = 1<br>
tabext = 1<br>
implicit_solvent = No<br>
gb_algorithm = Still<br>
gb_epsilon_solvent = 80<br>
nstgbradii = 1<br>
rgbradii = 2<br>
gb_saltconc = 0<br>
gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br>
gb_obc_gamma = 4.85<br>
sa_surface_tension = 2.092<br>
DispCorr = No<br>
free_energy = no<br>
init_lambda = 0<br>
sc_alpha = 0<br>
sc_power = 0<br>
sc_sigma = 0.3<br>
delta_lambda = 0<br>
nwall = 0<br>
wall_type = 9-3<br>
wall_atomtype[0] = -1<br>
wall_atomtype[1] = -1<br>
wall_density[0] = 0<br>
wall_density[1] = 0<br>
wall_ewald_zfac = 3<br>
pull = no<br>
disre = No<br>
disre_weighting = Conservative<br>
disre_mixed = FALSE<br>
dr_fc = 1000<br>
dr_tau = 0<br>
nstdisreout = 100<br>
orires_fc = 0<br>
orires_tau = 0<br>
nstorireout = 100<br>
dihre-fc = 1000<br>
em_stepsize = 0.01<br>
em_tol = 10<br>
niter = 20<br>
fc_stepsize = 0<br>
nstcgsteep = 1000<br>
nbfgscorr = 10<br>
ConstAlg = Lincs<br>
shake_tol = 0.0001<br>
lincs_order = 4<br>
lincs_warnangle = 30<br>
lincs_iter = 1<br>
bd_fric = 0<br>
ld_seed = 1993<br>
cos_accel = 0<br>
deform (3x3):<br>
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
userint1 = 0<br>
userint2 = 0<br>
userint3 = 0<br>
userint4 = 0<br>
userreal1 = 0<br>
userreal2 = 0<br>
userreal3 = 0<br>
userreal4 = 0<br>
grpopts:<br>
nrdf: 11297<br>
ref_t: 300<br>
tau_t: 0.1<br>
anneal: No<br>
ann_npoints: 0<br>
acc: 0 0 0<br>
nfreeze: N N N<br>
energygrp_flags[ 0]: 0<br>
efield-x:<br>
n = 0<br>
efield-xt:<br>
n = 0<br>
efield-y:<br>
n = 0<br>
efield-yt:<br>
n = 0<br>
efield-z:<br>
n = 0<br>
efield-zt:<br>
n = 0<br>
bQMMM = FALSE<br>
QMconstraints = 0<br>
QMMMscheme = 0<br>
scalefactor = 1<br>
qm_opts:<br>
ngQM = 0<br>
Table routines are used for coulomb: TRUE<br>
Table routines are used for vdw: FALSE<br>
Will do PME sum in reciprocal space.<br>
<br>
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen<br>
A smooth particle mesh Ewald method<br>
J. Chem. Phys. 103 (1995) pp. 8577-8592<br>
-------- -------- --- Thank You --- -------- --------<br>
<br>
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br>
Cut-off's: NS: 1 Coulomb: 1 LJ: 2<br>
System total charge: -0.000<br>
Generated table with 1500 data points for Ewald.<br>
Tabscale = 500 points/nm<br>
Generated table with 1500 data points for LJ6.<br>
Tabscale = 500 points/nm<br>
Generated table with 1500 data points for LJ12.<br>
Tabscale = 500 points/nm<br>
Configuring nonbonded kernels...<br>
Testing AMD 3DNow support... not present.<br>
Testing ia32 SSE support... present.<br>
<br>
<br>
Removing pbc first time<br>
<br>
Initializing LINear Constraint Solver<br>
<br>
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>
LINCS: A Linear Constraint Solver for molecular simulations<br>
J. Comp. Chem. 18 (1997) pp. 1463-1472<br>
-------- -------- --- Thank You --- -------- --------<br>
<br>
The number of constraints is 5500<br>
Center of mass motion removal mode is Linear<br>
We have the following groups for center of mass motion removal:<br>
0: rest<br>
<br>
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
G. Bussi, D. Donadio and M. Parrinello<br>
Canonical sampling through velocity rescaling<br>
J. Chem. Phys. 126 (2007) pp. 014101<br>
-------- -------- --- Thank You --- -------- --------<br>
<br>
There are: 5600 Atoms<br>
Max number of connections per atom is 4<br>
Total number of connections is 11000<br>
Max number of graph edges per atom is 4<br>
Total number of graph edges is 11000<br>
<br>
Constraining the starting coordinates (step 0)<br>
<br>
Constraining the coordinates at t0-dt (step 0)<br>
RMS relative constraint deviation after constraining: 6.33e-04<br>
Initial temperature: 306.393 K<br>
<br>
Started mdrun on node 0 Thu Oct 8 09:58:49 2009<br>
<br>
Step Time Lambda<br>
0 0.00000 0.00000<br>
<br>
Grid: 25 x 25 x 25 cells<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.0.2<br>
Source code file: constr.c, line: 136<br>
<br>
Fatal error:<br>
Too many LINCS warnings (3821)<br>
If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br>
or set the environment variable GMX_MAXCONSTRWARN to -1,<br>
but normally it is better to fix the problem<br>
-------------------------------------------------------<br>
<br>
Can anyone help me to navigate this issue?<br>
Thanks<br>
-- <br>
Yongchul "Greg" Chung<br>
Graduate Student<br>
Dept. of Chemical Engineering, Case Western Reserve University<br></div></div><div class="im">
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></blockquote><font color="#888888">
<br>
<br>
-- <br>
---------------------------------------------------<br>
Dr. Jochen Hub<br>
Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4714451 Fax: +46-18-511755</font><div><div></div><div class="h5"><br>
---------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yongchul "Greg" Chung<br>Graduate Student<br>Dept. of Chemical Engineering, Case Western Reserve University<br>