Hi,<br>Here's my mdp file:<br><br>*********************************+<br>title = Martini<br>integrator = md<br>tinit = 0.0<br>dt = 0.03<br>nsteps = 200000<br>nstcomm = 1<br>nstxout = 1000<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 1000<br>nstenergy = 100<br>nstxtcout = 1000<br>xtc_precision = 100<br>energygrps = NN<br>nstlist = 10<br>ns_type = grid<br> pbc = xyz<br>rlist = 1.4<br>coulombtype = Shift<br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift<br>rvdw_switch = 0.9<br>rvdw = 1.2<br>DispCorr = No<br>tcoupl = Berendsen<br>tau_t = 0.1<br>tc-grps = NN<br>ref_t = 100<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 473529<br>constraints = none<br>constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br>lincs_warnangle = 30<br>***********************************<br><br>and my top file:<br>*************************<br>#include "martini_v21.itp"<br>#include "nn_num.itp"<br><br>[ system ]<br>NN CHAIN<br><br>[ molecules ]<br>NN 1<br>**************************<br><br>where the nn_num.itp looks like:<br><br>************************************<br>;<br>; Topology file for NN<br>;<br>;<br>[ moleculetype ]<br>; Name nrexcl<br>NN 1<br><br> [atoms]<br>; id<br> 1 C1 1 NN S01 1 0.0<br> 2 P4 1 NN P02 2 0.0<br> 3 C1 1 NN B03 3 0.0<br> 4 P4 1 NN P04 4 0.0<br> 5 C1 1 NN B05 5 0.0<br>..............................<br> [bonds]<br>; i j funct table_nr force.c.<br> 1 2 8 0 1.0<br> 2 3 8 0 1.0<br> 3 4 8 0 1.0<br> 4 5 8 0 1.0<br> 5 6 8 0 1.0<br> 6......................<br>.................................<br>[angles]<br>; i j k funct r0 force.c.<br> 1 2 3 2 180.000 25.000<br> 2 3 4 2 180.000 25.000<br> 3 4 5 2 180.000 25.000<br> 4 5 6 2 180.000 25.000<br> 5 6 7 2 180.000 25.000<br> 6 7 8 2 180.000 <br> .........................................<br><br>************************************************<br>Thank you<br><br>AM<br>
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----Messaggio originale----<br>Da: Mark.Abraham@anu.edu.au<br>Data: 5-ott-2009 11.19 PM<br>A: "Discussion list for GROMACS users"<gmx-users@gromacs.org><br>Ogg: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem<br><br>albitauro@virgilio.it wrote:<br>> Hi,<br>> I came back to my original stretching potential in tabulated form and I <br>> have still problems...<br>> when running a geometry optimization the results are like that:<br>> <br>> *************************************************<br>> ^MStep 635, Epot=2.259501e+02, Fnorm=4.086e+00, Fmax=1.886e+01 (atom 34)<br>> ^MStep 636, Epot=2.259499e+02, Fnorm=3.847e+00, Fmax=1.992e+01 (atom 33)<br>> ^MStep 637, Epot=2.259495e+02, Fnorm=1.002e+01, Fmax=5.408e+01 (atom 33)<br>> ^MStep 638, Epot=2.259449e+02, Fnorm=1.026e+01, Fmax=4.098e+01 (atom 34)<br>> ^MStep 639, Epot=2.259393e+02, Fnorm=2.193e+01, Fmax=1.159e+02 (atom 35)<br>> ^MStep 640, Epot=2.259364e+02, Fnorm=1.469e+01, Fmax=7.064e+01 (atom 34)<br>> ^MStep 641, Epot=2.259335e+02, Fnorm=1.281e+01, Fmax=7.154e+01 (atom 34)<br>> ^MStep 642, Epot=2.259315e+02, Fnorm=5.803e+00, Fmax=2.861e+01 (atom 35)<br>> ^MStep 643, Epot=2.259314e+02, Fnorm=6.332e+00, Fmax=3.116e+01 (atom 34)<br>> ^MStep 644, Epot=2.259310e+02, Fnorm=3.550e+00, Fmax=1.502e+01 (atom 34)<br>> <br>> Stepsize too small, or no change in energy.<br>> Converged to machine precision,<br>> but not to the requested precision Fmax < 0.1<br>> ************************************************************************************<br>> <br>> as if the system is frozen. My system here is an isolated, linear and <br>> finite-length chain.<br>> When running an md simulation I got the error:<br>> <br>> -------------------------------------------------------<br>> Program mdrun_mpi, VERSION 4.0.5<br>> Source code file: bondfree.c, line: 1772<br>> <br>> Fatal error:<br>> A tabulated bond interaction table number 0 is out of the table range: r <br>> 1.815411, between table indices 1815 and 1816, table length 1001<br>> -------------------------------------------------------<br>> <br>> The tabulated potential is uniformly spaced, the bond type is 8 to <br>> exclude LJ interaction between bonded atoms, nrexcl=1 to include 1-3 <br>> interactions (as required by MARTINI force field). <br><br>That seems like it should work.<br><br>> The same system does <br>> not have any problem when running simulation with an harmonic stretching <br>> potential in both numerical and analytical form.<br>> Does anyone have any suggestion for possible solutions or error in the <br>> input?<br><br>Running gmxcheck between various .tpr files may be instructive, e.g. one <br>file may have many more nonbonded interactions, or such. Otherwise, <br>posting your .mdp file and the start of your .top may help us spot a <br>problem.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br>