[gmx-users] How to use tabulated potentials to do coarse grained simulation?

[Berk Hess]

Hi,

You potential is zero, since all your force-field parameters are zero.
Your should use g or h (not f, since this is the electrostatics function)
and set c6 or c12 (when using g or h) to 1.
See eq. 6.21 in the manual.

Berk.


> Date: Mon, 26 May 2008 21:40:50 +0800
> From: catfish.hku at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] How to use tabulated potentials to do coarse grained	simulation?
> 
> Dear all,
> 
> I am doing the coarse grained simulation of a water box.
> I have generated the tabulated potential between water molecules and
> planing to write codes to do coarse grained simulation.
> Fortunately, the experts on the gmx-dev maillist told me that I can
> use the tabulated function provided by Gromacs.
> 
> the following is what I have done step by step:
> 1. prepare the table_SOL_SOL.xvg(7columns, r,f,f',g,g',h,h')
> as I combined all the potentials into one term, the g, g' and h,h' are
> all set to zeros.
> 2. prepare the WAT.gro and WAT.top
> 3. edit the md.mdp
> 4. grompp -f md.mdp -c WAT.gro -p WAT.top -o md.tpr
> 5. mdrun -deffnm md -table table
> However, at step 5, I kept on getting the following error messages:
> Reading file CGMD.tpr, VERSION 3.3 (single precision)
> Segmentation fault
> 
> can anyone tell me what is wrong with my input files?
> THanks  a lot
> 
> the content of WAT.top:
> =======================
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>   1             1               no              1.0     1.0
> 
> [ atomtypes ]
> ;name  mass      charge  ptype       c6           c12
> W1    18.01540    0.0   A            0.0          0.0
> 
> [ moleculetype ]
> ; molname       nrexcl
> WAT              1
> 
> [ atoms ]
> ; id    at type res nr  residu name     at name  cg nr   charge
> 1       W1       1       SOL              WAT        1       0
> 
> [ system ]
> ; Name
> WATER CG BOX
> 
> [ molecules ]
> ; Compound        #mols
> WAT                1728
> ================================================
> 
> the content ot md.mdp:
> ================================================
> title = waterbox MD simulation
> cpp = /usr/bin/cpp ; location of cpp on linux
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 10 ps.
> nstcomm = 1
> nstxout = 1000 ; output coordinates every 2 ps; 500 out put only
> nstvout = 0
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 0.8
> coulombtype = User
> rcoulomb = 0.8
> vdwtype = User
> rvdw = 0.8
> 
> table-extension = 0.8 ;nm
> energygrp_table = SOL SOL
> 
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on
> Tcoupl = berendsen
> tau_t = 0.1
> tcgrps = SOL
> ref_t = 300
> tcgrps = SOL
> ref_t = 300
> ; Use Energy group monitoring
> energygrps = SOL
> ; Pressure coupling is on
> Pcoupl = no
> pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> ================================================
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