[gmx-users] Re: how to turn off the interamolecular interaction

[xianghong qi]

Hi, Mark,

I use the command: grompp -f md.mdp -c eq2.gro -p conf.top -n md.ndx -o
md.tpr -t eq2.trr
and index file was makde from command make_ndx, I named the two methanes as
methane1 and methane2.
and my mdp file is :

integrator               = sd
ld_seed                  = -1
; start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 25000000
; number of steps for center of mass motion removal =
nstcomm                  = 100
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 25000000
nstvout                  = 25000000
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 500 ; every 1 ps
nstenergy                = 50000 ; every 100 ps
; Output frequency and precision for xtc file
nstxtcout                = 50 ; every 0.1 ps
xtc-precision            = 10000
xtc_grps                 = system
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz or none
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0
domain-decomposition     = no
; Turn off intermolecular interaction between CH4:
energygrp_excl           = Methane1 Methane2
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
;rcoulomb-switch          = 0
rcoulomb                 = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r                = 1
; Method for doing Van der Waals
vdw-type                 = switch
; cut-off lengths
rvdw                     = 0.9
rvdw-switch              = 0.8
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; OPTIONS FOR TEMPERATURE COUPLING
tc_grps                  = system
tau_t                    = 1.0  ; Langevin friction constant (ps)
ref_t                    = 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = No
pcoupltype               = isotropic
tau_p                    = 5.0
compressibility          = 4.5e-05
ref_p                    = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
; OPTIONS FOR BONDS
constraints              = hbonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = yes
*******************************************************
I can't understand why Methane1 is not an energy group.
Thanks for your help.
-Xianghong Qi





On Wed, Nov 19, 2008 at 3:04 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> xianghong qi wrote:
>
>> Hi, Mark:
>>  I made the index file and call two methanes as methane1 and methane2 ,
>> then I set energygrp_excl = methane1 methane2, but when I run grompp, it
>> said methane1 is not an energy group. What do you understand this problem?
>> Thanks. -Xianghong Qi
>>
>
> You haven't done what you think you've done. I can't tell what you've done
> wrong because you haven't told me what you've done, i.e. examples and
> command lines. My guess is that you didn't supply your index file to grompp,
> so it can't tell what the definition is.
>
>
> Mark
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