[gmx-users] For GMX implicit solvent MD

[Justin Lemkul]

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
>

-- 
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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

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