On 11/28/13 9:31 AM, dxl...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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