[gmx-users] Energy minimisation
JMandumpal
jesbman at rediffmail.com
Tue Dec 4 08:23:31 CET 2007
Dear Gromacs users,
Thanks for the messages.
Tsjerk,
I was not aware that capital letters denote unpolite. I just used them to highlight the problem so others can easily pick out. Thanks for the suggestions as well.
I modified the file:
*******************************************************************
cpp = /lib/cpp
define = -DPOSRES -DFLEX_SPC
constraints = none
morse = no
integrator = steep
nsteps = 2000
; Energy minimizing
emtol = 100
emstep = 0.00001
nstcomm = 1
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.8
coulombtype = pme
rcoulomb = 0.8
vdw-type = cut-off
rvdw = 0.8
nstenergy = 10
Tcoupl = no
Pcoupl = no
gen_vel = no
*************************************************
But the message is the same.
As Dallas and others mentioned, I attach the last part of myt .gro file
*****************************************************************
245SOL LP2 1225 0.977 -0.910 0.116
246SOL OW 1226 0.927 -0.946 0.484
246SOL HW1 1227 0.985 -0.880 0.447
246SOL HW2 1228 0.852 -0.950 0.425
246SOL LP1 1229 0.907 -0.928 0.549
246SOL LP2 1230 0.960 -1.008 0.487
247SOL OW 1231 0.970 -0.641 -0.228
247SOL HW1 1232 1.010 -0.704 -0.169
247SOL HW2 1233 1.006 -0.556 -0.201
247SOL LP1 1234 0.900 -0.642 -0.221
247SOL LP2 1235 0.986 -0.655 -0.295
248SOL OW 1236 0.953 -0.556 0.247
248SOL HW1 1237 1.010 -0.481 0.233
248SOL HW2 1238 1.010 -0.624 0.284
248SOL LP1 1239 0.925 -0.578 0.186
248SOL LP2 1240 0.901 -0.540 0.292
249SOL OW 1241 0.974 -0.356 -0.452
249SOL HW1 1242 1.010 -0.438 -0.485
249SOL HW2 1243 1.010 -0.347 -0.364
249SOL LP1 1244 0.904 -0.359 -0.450
249SOL LP2 1245 0.993 -0.302 -0.493
250SOL OW 1246 0.981 -0.228 0.866
250SOL HW1 1247 1.010 -0.229 0.957
250SOL HW2 1248 1.010 -0.312 0.831
250SOL LP1 1249 1.010 -0.175 0.831
250SOL LP2 1250 0.911 -0.223 0.863
251SOL OW 1251 0.979 -0.053 -0.717
251SOL HW1 1252 0.884 -0.039 -0.721
251SOL HW2 1253 1.006 -0.053 -0.809
251SOL LP1 1254 0.994 -0.114 -0.686
251SOL LP2 1255 1.010 -0.001 -0.682
252SOL OW 1256 0.981 0.286 -0.345
252SOL HW1 1257 1.010 0.289 -0.254
252SOL HW2 1258 1.010 0.369 -0.383
252SOL LP1 1259 0.911 0.281 -0.349
252SOL LP2 1260 1.010 0.232 -0.379
253SOL OW 1261 0.968 0.619 -0.698
253SOL HW1 1262 0.886 0.667 -0.704
253SOL HW2 1263 0.942 0.531 -0.672
253SOL LP1 1264 1.010 0.648 -0.649
253SOL LP2 1265 1.002 0.618 -0.759
254SOL OW 1266 0.981 0.543 -0.103
254SOL HW1 1267 1.010 0.467 -0.054
254SOL HW2 1268 1.010 0.618 -0.051
254SOL LP1 1269 0.911 0.544 -0.110
254SOL LP2 1270 1.010 0.545 -0.167
255SOL OW 1271 0.985 0.378 0.613
255SOL HW1 1272 1.010 0.327 0.690
255SOL HW2 1273 0.890 0.377 0.613
255SOL LP1 1274 1.010 0.348 0.555
255SOL LP2 1275 1.010 0.443 0.617
256SOL OW 1276 0.981 0.516 0.287
256SOL HW1 1277 1.010 0.572 0.215
256SOL HW2 1278 1.010 0.562 0.366
256SOL LP1 1279 1.010 0.453 0.283
256SOL LP2 1280 0.911 0.510 0.287
257SOL OW 1281 0.847 0.408 0.942
257SOL HW1 1282 0.841 0.466 0.866
257SOL HW2 1283 0.941 0.407 0.964
257SOL LP1 1284 0.825 0.344 0.926
257SOL LP2 1285 0.810 0.433 0.996
258SOL OW 1286 0.983 0.951 0.741
258SOL HW1 1287 0.888 0.947 0.746
258SOL HW2 1288 1.001 1.010 0.668
258SOL LP1 1289 1.010 0.888 0.728
258SOL LP2 1290 1.010 0.976 0.800
0.00000 0.00000 0.00000
"out.gro" 1293L, 58138C
********************************************
the system is tip5p water molecule.
regards,
Jestin Mandumpal
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071204/07707aa1/attachment.html>
More information about the gromacs.org_gmx-users
mailing list