On 10/1/12 7:10 AM, Ali Alizadeh wrote:
Dear all users
1- I am trying to simulate a system that contains 1182 methane
molecules(5910 atoms) and 1830 water molecules(5490), I
keep getting these errors.
Something is wrong with the starting configuration, topology, or .mdp settings
(see below for comments) such that energy minimization fails almost instantly.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
2- Gromacs does not give me a .xtc file, Why?
Perhaps there's some quirk of the code that won't produce an .xtc file with an
EM algorithm. EM is normally quick and takes up little disk space, so the
benefit to having a compressed trajectory is minimal in most cases.
My command lines for grompp and mdrun in terminal window:
grompp -f npt.mdp -c wwfull.top.gro -p topol.top -o topol.tpr -n ww.ndx
mdrun -s topol.tpr -o wwfull.trr -x wwfull.xtc
These are errors and my .mdp file:
...........................................
Steepest Descents:
Tolerance (Fmax) = 1.00000e-04
Number of steps = 1000
Step 50, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000589, max 0.014000 (between atoms 2636 and 2638)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2636 2637 39.4 0.1090 0.1092 0.1090
Step 51, time 0.0102 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001802, max 0.029832 (between atoms 2026 and 2029)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2331 2334 43.1 0.1090 0.1093 0.1090
2026 2028 49.6 0.1090 0.1095 0.1090
5071 5074 41.7 0.1090 0.1093 0.1090
4806 4808 47.0 0.1090 0.1095 0.1090
Step 52, time 0.0104 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003002, max 0.049492 (between atoms 156 and 159)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
471 474 51.7 0.1090 0.1096 0.1090
2331 2334 32.4 0.1093 0.1078 0.1090
5071 5074 31.3 0.1093 0.1081 0.1090
156 160 55.3 0.1090 0.1095 0.1090
916 919 41.0 0.1090 0.1093 0.1090
5886 5890 61.1 0.1090 0.1092 0.1090
Step 53, time 0.0106 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034606, max 0.843079 (between atoms 5886 and 5890)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
471 475 31.5 0.1049 0.1325 0.1090
471 474 92.9 0.1096 0.1519 0.1090
471 473 38.6 0.1044 0.1402 0.1090
471 472 92.7 0.1048 0.1568 0.1090
2331 2335 48.8 0.1082 0.1083 0.1090
2331 2334 48.4 0.1078 0.1070 0.1090
2331 2333 88.8 0.1110 0.1564 0.1090
2331 2332 88.8 0.1110 0.1586 0.1090
2026 2030 89.4 0.1103 0.1177 0.1090
2026 2028 40.0 0.1091 0.1191 0.1090
2026 2027 38.2 0.1089 0.1207 0.1090
5071 5075 41.9 0.1084 0.1048 0.1090
5071 5074 41.6 0.1081 0.1043 0.1090
5071 5073 88.6 0.1109 0.1376 0.1090
5071 5072 88.7 0.1110 0.1392 0.1090
4806 4810 89.3 0.1104 0.1176 0.1090
4806 4809 32.7 0.1104 0.0927 0.1090
4806 4808 35.2 0.1089 0.1140 0.1090
4806 4807 35.0 0.1088 0.1153 0.1090
156 160 92.7 0.1095 0.1324 0.1090
156 159 80.8 0.1036 0.0523 0.1090
156 158 90.0 0.1036 0.1338 0.1090
156 157 90.4 0.1037 0.1489 0.1090
2276 2280 38.3 0.1091 0.1114 0.1090
2276 2277 33.0 0.1089 0.1134 0.1090
2286 2290 37.8 0.1090 0.1102 0.1090
916 920 90.1 0.1068 0.1704 0.1090
916 919 45.9 0.1093 0.1237 0.1090
916 917 65.0 0.1067 0.1285 0.1090
1296 1300 31.2 0.1090 0.1094 0.1090
5886 5890 90.9 0.1092 0.2009 0.1090
5886 5889 47.9 0.1043 0.1326 0.1090
5886 5888 85.9 0.1045 0.1282 0.1090
5886 5887 91.4 0.1046 0.1208 0.1090
Back Off! I just backed up step53b_n0.pdb to ./#step53b_n0.pdb.1#
Back Off! I just backed up step53c_n0.pdb to ./#step53c_n0.pdb.1#
Wrote pdb files with previous and current coordinates
..
..
..
This is my .mdp file:
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit = 0
dt = 0.0002
nsteps = 1000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm_mode = Linear
; number of steps for center of mass motion removal
nstcomm = 10
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 0.0001
Note that you will never achieve this value with single precision (or likely
ever, for that matter).
emstep = 0.00001
Something doesn't gel here. The step size indicated in the mdrun output above
suggests that your emstep is much larger than this value. Note that dt is not
used in conjunction with EM algorithms.
; Max number of iterations in relax_shells
niter = 100
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1
nstvout = 100
nstfout = 100
nstcalcenergy = -1
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 250
nstenergy = 60
; Output frequency and precision for xtc file
nstxtcout = 1
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc_grps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 20
nstlist should always be set to 1 for EM.
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.35
rlistlong = 0.35 ; cut off distance for
These cutoff settings make no sense.
short range neighbor list
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.35
Same comment here regarding rcoulomb. You can't just choose arbitrary values
for these settings and hope they work. Force fields require certain cutoff
values. If you don't know them, spend some time reading about your chosen force
field - it will save you a lot of time and wasted data in the future.
; Method for doing Van der Waals
vdw_type = Cut-off
; cut-off lengths
rvdw_switch = 0
rvdw = 0.35
Same comment regarding rvdw.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
