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

[David]

On Wed, 2005-04-27 at 19:23 +0100, Joanne Hanna wrote:
> 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
This is a warning, not an error. And this is what you want in vacuum.
Your current setup will simulate computing all interactions, no cutoff.
Which means you can also turn off temperature coupling.

> 
> 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                     = 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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