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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>You potential is zero, since all your force-field parameters are zero.<br>Your should use g or h (not f, since this is the electrostatics function)<br>and set c6 or c12 (when using g or h) to 1.<br>See eq. 6.21 in the manual.<br><br></div>Berk.<br><br><br><hr id="stopSpelling">> Date: Mon, 26 May 2008 21:40:50 +0800<br>> From: catfish.hku@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] How to use tabulated potentials to do coarse grained simulation?<br>> <br>> Dear all,<br>> <br>> I am doing the coarse grained simulation of a water box.<br>> I have generated the tabulated potential between water molecules and<br>> planing to write codes to do coarse grained simulation.<br>> Fortunately, the experts on the gmx-dev maillist told me that I can<br>> use the tabulated function provided by Gromacs.<br>> <br>> the following is what I have done step by step:<br>> 1. prepare the table_SOL_SOL.xvg(7columns, r,f,f',g,g',h,h')<br>> as I combined all the potentials into one term, the g, g' and h,h' are<br>> all set to zeros.<br>> 2. prepare the WAT.gro and WAT.top<br>> 3. edit the md.mdp<br>> 4. grompp -f md.mdp -c WAT.gro -p WAT.top -o md.tpr<br>> 5. mdrun -deffnm md -table table<br>> However, at step 5, I kept on getting the following error messages:<br>> Reading file CGMD.tpr, VERSION 3.3 (single precision)<br>> Segmentation fault<br>> <br>> can anyone tell me what is wrong with my input files?<br>> THanks a lot<br>> <br>> the content of WAT.top:<br>> =======================<br>> [ defaults ]<br>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>> 1 1 no 1.0 1.0<br>> <br>> [ atomtypes ]<br>> ;name mass charge ptype c6 c12<br>> W1 18.01540 0.0 A 0.0 0.0<br>> <br>> [ moleculetype ]<br>> ; molname nrexcl<br>> WAT 1<br>> <br>> [ atoms ]<br>> ; id at type res nr residu name at name cg nr charge<br>> 1 W1 1 SOL WAT 1 0<br>> <br>> [ system ]<br>> ; Name<br>> WATER CG BOX<br>> <br>> [ molecules ]<br>> ; Compound #mols<br>> WAT 1728<br>> ================================================<br>> <br>> the content ot md.mdp:<br>> ================================================<br>> title = waterbox MD simulation<br>> cpp = /usr/bin/cpp ; location of cpp on linux<br>> constraints = all-bonds<br>> integrator = md<br>> dt = 0.002 ; ps !<br>> nsteps = 5000 ; total 10 ps.<br>> nstcomm = 1<br>> nstxout = 1000 ; output coordinates every 2 ps; 500 out put only<br>> nstvout = 0<br>> nstfout = 0<br>> nstlist = 10<br>> ns_type = grid<br>> rlist = 0.8<br>> coulombtype = User<br>> rcoulomb = 0.8<br>> vdwtype = User<br>> rvdw = 0.8<br>> <br>> table-extension = 0.8 ;nm<br>> energygrp_table = SOL SOL<br>> <br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> ; Berendsen temperature coupling is on<br>> Tcoupl = berendsen<br>> tau_t = 0.1<br>> tcgrps = SOL<br>> ref_t = 300<br>> tcgrps = SOL<br>> ref_t = 300<br>> ; Use Energy group monitoring<br>> energygrps = SOL<br>> ; Pressure coupling is on<br>> Pcoupl = no<br>> pcoupltype = isotropic<br>> tau_p = 0.5<br>> compressibility = 4.5e-5<br>> ref_p = 1.0<br>> ; Generate velocites is on at 300 K.<br>> gen_vel = yes<br>> gen_temp = 300.0<br>> gen_seed = 173529<br>> ================================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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 /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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