[gmx-users] For GMX implicit solvent MD

[dxli75 at hotmail.com]

Dear all，
         I have changed the is.mdp file as following, However, the same error still can't be removed.
         What can I do for the simulation?
title = spc water
cpp = /usr/bin/cpp
;define = -DFLEXIBLE
constraints = all-bonds
integrator = md
tinit = 0
dt = 0.002 ; ps !
nsteps = 2000 ;
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 10
nstcalcenergy = 10
nstlist = 10
ns_type = grid
rlist = 0
pbc = no
coulombtype = cut-off;
rcoulomb = 0
vdwtype = cut-off
rvdw = 0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = gbsa
gb_algorithm = OBC;HCT;Still
nstgbradii = 1
rgbradii = 0
gb_epsilon_solvent = 80
gb_saltconc = 10
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.268 ;2.058/2.268
; Temperature coupling is on in two groups
Tcoupl = v-rescale
tau_t = 0.1
tc_grps = system
ref_t = 240
; Pressure coupling is off
Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = COM
; Generate velocites is on at 240 K.
gen_vel = no
gen_temp = 240.0
gen_seed = 173529





--

xiyuan
P.I.,Laboratory of Computational Biology
University of Shanghai for Science & Technology

At 2013-11-28 22:46:28,"Justin Lemkul" <jalemkul at vt.edu> wrote: > > >On 11/28/13 9:31 AM, dxli75 at hotmail.com wrote: >> Dear All, >>       I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD，it goes very well. Then when I use two SPC water molecules，it give me a Fatal error: >> Fatal error: >> Death & horror! GB generic interaction not implemented. >> > >Can you please provide the full fatal error, including the referenced source file? > >>         Can the GMX perform only a single molecule? > >In theory it should be able to handle anything. > >>         What's wrong with my MD? >> Attachment: >> # cat water-spc.gro >> Protein >> 6 >> 1SOL OW 1 0.502 0.516 0.052 -0.0106 -0.1291 -0.1474 >> 1SOL HW1 2 0.432 0.548 -0.012 -0.9087 1.3904 1.5119 >> 1SOL HW2 3 0.459 0.478 0.133 1.0765 0.6585 0.8283 >> 2SOL OW 1 0.512 0.516 0.052 -0.0106 -0.1291 -0.1474 >> 2SOL HW1 2 0.442 0.548 -0.012 -0.9087 1.3904 1.5119 >> 2SOL HW2 3 0.469 0.478 0.133 1.0765 0.6585 0.8283 >> 5.00000 5.00000 5.00000 >> >> # cat prmd-is.mdp >> title = water >> cpp = /usr/bin/cpp >> define = -DPOSRES_ICE >> ;define = -DFLEXIBLE >> constraints = all-bonds >> integrator = md >> tinit = 0 >> dt = 0.002 ; ps ! >> nsteps = 2000 ; total 0.100 ns >> nstxout = 1000 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 100 >> nstenergy = 10 >> nstcalcenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> pbc = xyz;no >> coulombtype = cut-off; >> rcoulomb = 1.0 >> vdwtype = cut-off >> rvdw = 1.2 > >Note that finite cutoffs with PBC are a bad approach for running implicit  >solvent simulations.  Use infinite cutoffs and no PBC. > >-Justin > >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 6 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; IMPLICIT SOLVENT ALGORITHM >> implicit_solvent = gbsa >> gb_algorithm = OBC;HCT;Still >> nstgbradii = 1 >> rgbradii = 1.0 >> gb_epsilon_solvent = 80 >> gb_saltconc = 10 >> gb_obc_alpha = 1 >> gb_obc_beta = 0.8 >> gb_obc_gamma = 4.85 >> gb_dielectric_offset = 0.009 >> sa_algorithm = Ace-approximation >> sa_surface_tension = 2.268 ;2.058/2.268 >> ; Temperature coupling is on in two groups >> Tcoupl = v-rescale >> tau_t = 0.1 >> tc_grps = system >> ref_t = 240 >> ; Pressure coupling is off >> Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No >> pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> refcoord_scaling = COM >> ; Generate velocites is on at 240 K. >> gen_vel = no >> gen_temp = 240.0 >> gen_seed = 173529 >> >> >> Your sincerely, >> >> -- >> >> Xiyuan >> > >--  >================================================== > >Justin A. Lemkul, Ph.D. >Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 601 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalemkul at outerbanks.umaryland.edu | (410) 706-7441 > >================================================== >--  >Gromacs Users mailing list > >* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.