<br>Dear gmx experts,<br><br>I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. <br><br>The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS warning) with dt=0.002<br>
Program mdrun, VERSION 4.0.7<br>Source code file: constr.c, line: 136<br><br>Fatal error:<br>Too many LINCS warnings (1053)<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>It seems Fmax, Epot values are reasonable. . In the list archive I read this statement
        by Mr.Justin Lemskul:
        
        
        
<p style="margin-bottom: 0cm;"><font style="color: rgb(0, 0, 0);" color="#008000">"changing </font><font color="#008000"><span style="color: rgb(0, 0, 0);">cutoffs
haphazardly is a recipe for failure" but I have no idea how this works....</span><u><br></u></font></p>
<p style="margin-bottom: 0cm;" lang="en-US"><font face="Courier New, monospace"><font size="2"><font color="#008000"><span style="color: rgb(0, 0, 0);">I also reduced the timestep to 0.001 ps but it did not work. I even did not get those written pdb files I got from dt=0.002 I had a look at structures and they were like rings!!. (initially hezane had a linear structure). <br>
</span></font></font></font></p><p style="margin-bottom: 0cm;" lang="en-US">Thank you for your time and help in advance<br><font face="Courier New, monospace"><font size="2"><font color="#008000"><span style="color: rgb(0, 0, 0);"></span></font></font></font></p>
<br><br><u>em output file:</u><br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br>
Number of steps = 100<br>
Step= 0, Dmax= 1.0e-02 nm, Epot= 8.36824e+05 Fmax= 2.26627e+03, atom= 2947<br>Step= 1, Dmax= 1.0e-02 nm, Epot= 8.17823e+05 Fmax= 2.98349e+03, atom= 2007<br>
Step= 2, Dmax= 1.2e-02 nm, Epot= 7.87850e+05 Fmax= 2.24621e+03, atom= 2447<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 7.70259e+05 Fmax= 3.13292e+03, atom= 3127<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 7.50886e+05 Fmax= 2.87650e+03, atom= 3125<br>
Step= 5, Dmax= 2.1e-02 nm, Epot= 7.15803e+05 Fmax= 5.48652e+03, atom= 3127<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 6.59011e+05 Fmax= 2.97146e+03, atom= 3105<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 7.10849e+05 Fmax= 5.51243e+03, atom= 3127^MStep= 8, Dmax= 1.5e-02 nm, Epot= 6.38805e+05 Fmax= 3.87761e+03, atom= 3107<br>
Step= 9, Dmax= 1.8e-02 nm, Epot= 6.21481e+05 Fmax= 2.69101e+03, atom= 1687<br>Step= 10, Dmax= 2.1e-02 nm, Epot= 6.43071e+05 Fmax= 5.74780e+03, atom= 227^MStep= 11, Dmax= 1.1e-02 nm, Epot= 6.00633e+05 Fmax= 2.56262e+03, atom= 3107<br>
Step= 12, Dmax= 1.3e-02 nm, Epot= 5.86914e+05 Fmax= 2.40254e+03, atom= 1687<br>Step= 13, Dmax= 1.5e-02 nm, Epot= 5.85431e+05 Fmax= 4.58696e+03, atom= 3107<br>Step= 14, Dmax= 1.9e-02 nm, Epot= 5.61423e+05 Fmax= 2.94308e+03, atom= 3127<br>
Step= 15, Dmax= 2.2e-02 nm, Epot= 5.85550e+05 Fmax= 5.56128e+03, atom= 1827^MStep= 16, Dmax= 1.1e-02 nm, Epot= 5.43780e+05 Fmax= 1.91577e+03, atom= 3107<br>Step= 17, Dmax= 1.3e-02 nm, Epot= 5.42825e+05 Fmax= 3.49456e+03, atom= 4247<br>
Step= 18, Dmax= 1.6e-02 nm, Epot= 5.30046e+05 Fmax= 3.16969e+03, atom= 4247<br>Step= 19, Dmax= 1.9e-02 nm, Epot= 5.41307e+05 Fmax= 4.27646e+03, atom= 4247^MStep= 20, Dmax= 9.6e-03 nm, Epot= 5.14493e+05 Fmax= 1.28031e+03, atom= 3115<br>
Step= 21, Dmax= 1.2e-02 nm, Epot= 5.14984e+05 Fmax= 3.45692e+03, atom= 4247^MStep= 22, Dmax= 5.8e-03 nm, Epot= 5.07865e+05 Fmax= 1.27065e+03, atom= 3115<br>Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03, atom= 4247<br>
Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom= 4247Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03, atom= 4247<br>Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom= 4247<br>
Step= 25, Dmax= 1.0e-02 nm, Epot= 4.95017e+05 Fmax= 2.30502e+03, atom= 4247<br>Step= 26, Dmax= 1.2e-02 nm, Epot= 4.94561e+05 Fmax= 3.17535e+03, atom= 1847<br>Step= 27, Dmax= 1.4e-02 nm, Epot= 4.91526e+05 Fmax= 2.99909e+03, atom= 1847<br>
Step= 28, Dmax= 1.7e-02 nm, Epot= 5.00763e+05 Fmax= 4.45550e+03, atom= 1847^MStep= 29, Dmax= 8.6e-03 nm, Epot= 4.76093e+05 Fmax= 9.86600e+02, atom= 3115<br><br>writing lowest energy coordinates.<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>gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)<br>
<br><br><br><br>md parameter file:<br><br>title = Hexane<br>cpp = /lib/cpp<br><br>; Preprocessing<br>define = -DPOSRES<br><br>; Run control<br>integrator = md<br>
dt = 0.001 ; 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 = 1000<br>nstfout = 1<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 = PME<br>
vdw-type = cut-off<br>; Cut-off<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>topology file:<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><br>
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