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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