[gmx-users] Enzyme Simulation vacuum, No ligands, Non periodic system

[Joanne Hanna]

Hi

I have been trying to grompp my files to run a MD simulation on an enzyme in vacuum without ligands.
I have choosen the vacuum force field and have succesfully minimised the enzyme but cannot progress as i get many errors from grompp regarding cut-offs, relating to the values of nstcomm etc.

I have fixed a number of these errors by setting the ns_type to simple 
and also setting all of my cut offs to 0
although i am still using the coulombtype = cut-off option, which i'm not sure is the correct thing to do

I cannot however get around this error:

WARNING 1 [file md1.mdp, line unknown]:
mdrun will apply removal of angular momentum when nstcomm < 0
..........
..........
There was 1 warning

I have attached my *.mdp file below and am requesting any advice as to which options i should be choosing in the *.mdp file as i am now choosing options on a trial and error basis to try and minimise the errors!

Many thanks
Jo

##### md1.mdp ######

title                    = Enz No Ligands
cpp                      = /lib/cpp
define                   = -DPOSRES

integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 50000
nstcomm                  = -1
comm-grps                = 

nstxout                  = 100
nstvout                  = 500
nstfout                  = 0
 
nstlog                   = 10
nstenergy                = 10
 
nstxtcout                = 100
xtc-precision            = 100

energygrps               = PROTEIN 
 
nstlist                  = 10
ns-type                  = simple 
pbc                      = no 
rlist                    = 0.0
domain-decomposition     = no
 
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0.0
epsilon-r                = 1

; Van der Waals = 
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 0.0

DispCorr                 = No 
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0

tcoupl                   = berendsen
tc-grps                  = PROTEIN  
tau-t                    = 0.5 
ref-t                    = 0  
Pcoupl                   = no
annealing                = no 
;zero-temp_time           = 0

; GENERATE VELOCITIES FOR STARTUP RUN = 
gen-vel                  = yes
gen-temp                 = 310
gen-seed                 = 173529

constraints              = all-bonds 
constraint-algorithm     = Shake 
unconstrained-start      = yes 
shake-tol                = 0.00001 
lincs-order              = 4
step a bond =  
lincs-warnangle          = 30 
morse                    = no

disre                    = No
 Equal or Conservative = 
disre-weighting          = Equal 
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
nstdisreout              = 100

free-energy              = no
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0
sc-sigma                 = 0.3
 
acc-grps                 = 
accelerate               = 
freezegrps               = 
freezedim                = 
cos-acceleration         = 0
 
E-x                      = 
E-xt                     = 
E-y                      = 
E-yt                     = 
E-z                      = 
E-zt                     =