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Dear prof. Berk, Since it is the first time I use the tabulated potential, I have lots of questions about it. Could you help me out? Thanks a lot! I make the test in the system with only some waters between 2 implicit walls. 1. some related parameters of the .mdp file are listed below. Is there anything wrong? energygrps = SOL pbc = xy rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdw-type = cut-off rvdw = 1.2 DispCorr = EnerPres table-extension = 1 energygrp_table = ;Walls nwall = 2 wall_type = table wall_r_linpot = 0.0 wall_atomtype = opls_135 opls_135 wall_density = ;(the wall_density is included in the tabulated potential, right?) wall_ewald_zfac = 3 2. The flags of mdrun are: mdrun -deffnm table -tablep table_SOL_wall0.xvg table_SOL_wall1.xvg -table table.xvg where table.xvg is copied from gmx_top_path/table6-12.xvg, and table_SOL_wall0.xvg and table_SOL_wall1.xvg are the self-generated 9-3 potential (9-3 potential is used for the aim of testing and compare with the default 9-3 potential of gromacs.) Since I use only the tabulated potential between SOL-wall0 and SOL-wall1, why do I need the table.xvg? Does it affect the coulomb/vdw potential between SOL-SOL? 3. In the table_SOL_wall0.xvg and table_SOL_wall1.xvg, the distance range of 0-3nm is generated. max(rvdw, rcoulomb)=1.2 nm and table-extension=1. The question is what is the cutoff distance for the tabulated SOL-wall0/wall1 potential, 2.2nm or 3nm? 4. In the output file table.log, Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Reading user tables for 1 energy groups with 2 walls Read user tables from table_SOL_wall0.xvg with 1501 data points. Tabscale = 500 points/nm Read user tables from table_SOL_wall1.xvg with 1501 data points. Tabscale = 500 points/nm The question are: a) Since Table is not used for vdw (FALSE), why table is generated for LJ6/LJ12? b) Where does the value of "1100" data points come from? (Since rvdw=1.2, tabscale=500, it should be 1400, not 1100!?) c) 1501 data points is generated for table_SOL_wall0/wall1, the answer of the 3rd question (cutoff value for the tabulated potential calculation) should be 3nm, right? Sorry for the lots of questions! best wishes, Baofu Qiao Berk Hess wrote: Hi, Why not use the tabulated wall potential? That does not require are changes to the code.BerkDate: Tue, 5 Jan 2010 14:13:30 +0100 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] 10-4-3 implicit wall potential HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php_________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
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