[gmx-users] Box in Implicit Solvent Simulations

[Mark Abraham]

On 22/11/2011 10:08 PM, ifat shub wrote:
> Hi,
> I am running simulations using implicit solvent. I am using the pbc = 
> no option in my mdp file, however, I see it the .gro file that gromacs 
> is creating a box for the system.What is the effect of the box 
> in implicit solvent simulations?

None, if pbc = no. When writing a .gro file some data has to go into the 
space the format allows for the box. However the .mdp file controls 
whether that is significant. Later on when using analysis tools, some of 
the analyses might erroneously use that box if you don't give suitable 
instructions not to.

Mark

> This is the mdp file that I am using:
>
> ------run.mdp------
>
> integrator = md
>
> nsteps = 20000
>
> dt = 0.001
>
> implicit_solvent = GBSA
>
> pbc = no
>
> nstlist = 0
>
> ns_type = simple
>
> rlist = 0
>
> rgbradii = 0
>
> coulombtype = Cut-off
>
> rcoulomb = 0
>
> vdwtype = Cut-off
>
> rvdw = 0
>
> tcoupl = v-rescale
>
> tc_grps = system
>
> tau_t = 0.1
>
> ref_t = 1000
>
> energygrps = Protein_chain_A Protein_chain_C Protein_chain_E 
> Protein_chain_G Protein_chain_I Protein_chain_K
>
> gen_vel = yes
>
> gen_temp = 1000
>
> ld_seed = -1
>
> gen_seed = -1
>
> nstxout = 1
>
> nstvout = 1
>
> nstxtcout = 1
>
> nstenergy = 1
>
> ------------------
>
> Thanks,
> Ifat
> M.Sc. Student
> Bar Ilan University
> Ramat Gan
> Israel
>
>

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