Dear experts,<br><br>Could you please take a
look at energy values. The system contains only stack of hexane molecules. MD sun gives lincs warning. <br><br>1- How can I get rid of high repulsive potential? <br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cmoeed%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><style>
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</style><b><span style="font-size: 12pt; font-family: "Nimbus Roman No9 L";">genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist
1.1 0.55 0.55 -o Hexane-stack.gro</span></b><br><br><br>********------------------------***************************************************************************<br>energy minimization<br>my output.mdrun_em:<br><br>Steepest Descents converged to Fmax < 1000 in 30 steps<br>
Potential Energy = 4.76092783832156e+05<br>Maximum force = 9.86600079729483e+02 on atom 3115<br>Norm of force = 5.33725886931530e+02<br>*********************************************************************************************************<br>
g_energy file:<br><br>Statistics over 61 steps [ 0.0000 thru 0.1200 ps ], 12 data sets<br>
All averages are exact over 61 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>------------------------------<div id=":18o" class="ii gt">-------------------------------------------------<br>
Angle 78416.5 38731.2 25083.3 838187 102231<br>
LJ-14 1.16009e+08 8.87401e+08 8.87401e+08 3.06025e+06 373250<br>Coulomb-14 734.065 480.683 140.481 13056.3 1592.44<br>LJ (SR) 5482.29 5991.07 4445.16 114080 13914.1<br>
Coulomb (SR) 1711.47 732.288 228.708 -19758 -2409.83<br>Potential 1.16326e+08 8.8739e+08 8.8739e+08 921124 112347<br>Kinetic En. 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19 1.1871e+19<br>
Total Energy 1.77327e+18 5.4851e+18 4.28286e+18 9.73294e+19 1.1871e+19<br>Temperature 4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18 2.72133e+17<br>Pressure (bar) 1.48406e+15 4.59052e+15 3.58436e+15 8.14557e+16 9.93493e+15<br>
T-HEX 4.06507e+16 1.25741e+17 9.81811e+16 2.2312e+18 2.72133e+17<br>Lamb-HEX 0.99144 0.00206848 0 -0.0617392 -0.00753016<br>Heat Capacity Cv: -0.934076 J/mol K (factor = 9.56799)<br>
<br>*************** *************************************************************************<br><br>title = Hexane <br>cpp = /lib/cpp<br><br>; Run control<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 5000 ; total 1.0 ps.<br>nstcomm = 1 ; frequency for center of mass motion removal <br><br>; Output control<br>nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>
nstxout = 10 ; frequency to write coordinates/velocity/force to output trajectory file<br>nstvout = 0<br>nstfout = 10<br>nstlog = 10 ; frequency to write energies to log file<br>
<br>; Neighbor searching<br>nstlist = 10 ; neighborlist will be updated at least every 10 steps <br>;ns_type = grid<br><br>; Electrostatics/VdW<br>coulombtype = cut-off<br>
vdw-type = cut-off<br>; Cut-offs<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br><br>; Temperature coupling Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>tc-grps = HEX ;sol<br>tau_t = 0.1 ;0.1<br>ref_t = 300 ;300<br><br>; Pressure coupling: Pressure coupling is not on<br>
Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br><br>; Velocity generation Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes<br>
gen_temp = 300.0<br>gen_seed = 173529<br><br>; Bonds<br>constraints = all-bonds<br>constraint-algorithm = lincs<br><br>pbc=xyz<br><br>****************************************************************************************<br>
;<br>; File 'Hexane.top' was generated<br>; By user: moeed (500)<br>; On host: moeed-desktop<br>; At date: Thu Apr 8 13:51:19 2010<br>;<br>; This is your include topology file<br>; Generated by x2top<br>
;<br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>HEX 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18<br> 2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.3<br> 3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.42<br>
4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.54<br> 5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.66<br> 6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.84<br>
7 opls_140 1 HEX H1 6 0.06 1.008 ; qtot -0.78<br> 8 opls_140 1 HEX H2 6 0.06 1.008 ; qtot -0.72<br> 9 opls_140 1 HEX H3 6 0.06 1.008 ; qtot -0.66<br>
10 opls_140 1 HEX H4 5 0.06 1.008 ; qtot -0.6<br> 11 opls_140 1 HEX H5 5 0.06 1.008 ; qtot -0.54<br> 12 opls_140 1 HEX H6 4 0.06 1.008 ; qtot -0.48<br>
13 opls_140 1 HEX H7 4 0.06 1.008 ; qtot -0.42<br> 14 opls_140 1 HEX H8 3 0.06 1.008 ; qtot -0.36<br> 15 opls_140 1 HEX H9 3 0.06 1.008 ; qtot -0.3<br>
16 opls_140 1 HEX H10 2 0.06 1.008 ; qtot -0.24<br> 17 opls_140 1 HEX H11 2 0.06 1.008 ; qtot -0.18<br> 18 opls_140 1 HEX H12 1 0.06 1.008 ; qtot -0.12<br>
19 opls_140 1 HEX H13 1 0.06 1.008 ; qtot -0.06<br> 20 opls_140 1 HEX H14 1 0.06 1.008 ; qtot 0<br><br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br>
1 2 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05 <br> 1 18 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 1 19 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
1 20 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 2 3 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05 <br> 2 16 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
2 17 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 3 4 1 1.540000e-01 4.000000e+05 1.540000e-01 4.000000e+05 <br> 3 14 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
3 15 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 4 5 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05 <br> 4 12 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
4 13 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 5 6 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05 <br> 5 10 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
5 11 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 6 7 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br> 6 8 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br>
6 9 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05 <br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br> 1 4 1 <br> 1 14 1 <br> 1 15 1 <br>
2 5 1 <br> 2 12 1 <br> 2 13 1 <br> 3 6 1 <br> 3 10 1 <br> 3 11 1 <br> 3 18 1 <br> 3 19 1 <br> 3 20 1 <br> 4 7 1 <br> 4 8 1 <br>
4 9 1 <br> 4 16 1 <br> 4 17 1 <br> 5 14 1 <br> 5 15 1 <br> 6 12 1 <br> 6 13 1 <br> 7 10 1 <br> 7 11 1 <br> 8 10 1 <br> 8 11 1 <br>
9 10 1 <br> 9 11 1 <br> 10 12 1 <br> 10 13 1 <br> 11 12 1 <br> 11 13 1 <br> 12 14 1 <br> 12 15 1 <br> 13 14 1 <br> 13 15 1 <br> 14 16 1 <br>
14 17 1 <br> 15 16 1 <br> 15 17 1 <br> 16 18 1 <br> 16 19 1 <br> 16 20 1 <br> 17 18 1 <br> 17 19 1 <br> 17 20 1 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br>
2 1 18 1 1.120000e+02 4.000000e+02 1.120000e+02 4.000000e+02 <br> 2 1 19 1 1.110000e+02 4.000000e+02 1.110000e+02 4.000000e+02 <br> 2 1 20 1 1.110000e+02 4.000000e+02 1.110000e+02 4.000000e+02 <br>
18 1 19 1 1.070000e+02 4.000000e+02 1.070000e+02 4.000000e+02 <br> 18 1 20 1 1.070000e+02 4.000000e+02 1.070000e+02 4.000000e+02 <br> 19 1 20 1 1.080000e+02 4.000000e+02 1.080000e+02 4.000000e+02 <br>
1 2 3 1 1.130000e+02 4.000000e+02 1.130000e+02 4.000000e+02 <br> 1 2 16 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 1 2 17 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br>
3 2 16 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 3 2 17 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 16 2 17 1 1.060000e+02 4.000000e+02 1.060000e+02 4.000000e+02 <br>
2 3 4 1 1.130000e+02 4.000000e+02 1.130000e+02 4.000000e+02 <br> 2 3 14 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 2 3 15 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br>
4 3 14 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 4 3 15 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 14 3 15 1 1.060000e+02 4.000000e+02 1.060000e+02 4.000000e+02 <br>
3 4 5 1 1.130000e+02 4.000000e+02 1.130000e+02 4.000000e+02 <br> 3 4 12 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 3 4 13 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br>
5 4 12 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 5 4 13 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 12 4 13 1 1.060000e+02 4.000000e+02 1.060000e+02 4.000000e+02 <br>
4 5 6 1 1.130000e+02 4.000000e+02 1.130000e+02 4.000000e+02 <br> 4 5 10 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br> 4 5 11 1 1.100000e+02 4.000000e+02 1.100000e+02 4.000000e+02 <br>
6 5 10 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 6 5 11 1 1.090000e+02 4.000000e+02 1.090000e+02 4.000000e+02 <br> 10 5 11 1 1.060000e+02 4.000000e+02 1.060000e+02 4.000000e+02 <br>
5 6 7 1 1.110000e+02 4.000000e+02 1.110000e+02 4.000000e+02 <br> 5 6 8 1 1.110000e+02 4.000000e+02 1.110000e+02 4.000000e+02 <br> 5 6 9 1 1.120000e+02 4.000000e+02 1.120000e+02 4.000000e+02 <br>
7 6 8 1 1.080000e+02 4.000000e+02 1.080000e+02 4.000000e+02 <br> 7 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02 4.000000e+02 <br> 8 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02 4.000000e+02 <br>
<br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br> 18 1 2 3 3 3.600000e+02 5.000000e+00 3.000000e+00 3.600000e+02 5.000000e+00 3.000000e+00 <br>
1 2 3 4 3 3.600000e+02 5.000000e+00 3.000000e+00 3.600000e+02 5.000000e+00 3.000000e+00 <br> 2 3 4 5 3 3.600000e+02 5.000000e+00 3.000000e+00 3.600000e+02 5.000000e+00 3.000000e+00 <br>
3 4 5 6 3 3.600000e+02 5.000000e+00 3.000000e+00 3.600000e+02 5.000000e+00 3.000000e+00 <br> 4 5 6 7 3 3.600000e+02 5.000000e+00 3.000000e+00 3.600000e+02 5.000000e+00 3.000000e+00 <br>
<br>[ system ]<br>; Name<br>HEX<br><br>[ molecules ]<br>; Compound #mols<br>HEX 256<br><br><br><br><br></div><input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML">
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