[gmx-users] vaccum simulation error

[Erik Marklund]

Using a barostat for vaccum simulations is very peculiar.

Erik

On Feb 19, 2013, at 10:55 AM, Rajalakshmi.C wrote:

>
> hi all,
> i am trying to simulate polymer chains in solvent and vacuum media  
> using 45a3
> forcefield. for vacuum simulation i used different md parameters  
> than that of
> solvent media. first i put 100ps NVT and then 100ps NPT. i  
> sucessfully got NVT
> done but for NPT i got following error ,
>
> WARNING 1 [file npt-pr.mdp, line unknown]:
>  Turning off pressure coupling for vacuum system
>
>
> NOTE 1 [file npt-pr.mdp, line unknown]:
>  Tumbling and or flying ice-cubes: We are not removing rotation around
>  center of mass in a non-periodic system. You should probably set
>  comm_mode = ANGULAR.
>
> Too many warnings (1), grompp_mpicc terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> the parameters for NPT are;
> nstlist                  = 10
> ns-type                  = simple
> pbc                      = no
> rlist                    = 0
> coulombtype              = cut-off
> rcoulomb                 = 0
> fourierspacing		 = 0.12
> vdw-type                 = cut-off
> pme_order                = 4
> rvdw                     = 0
> ewald_rtol               = 0.00001
> Tcoupl                   = v-rescale
> tc-grps                  = PMH	
> tau_t                    = 0.1      	
> ref_t                    = 300
> Pcoupl                   = Berendsen
> Pcoupltype               = Isotropic
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> DispCorr                 = no
>
> can anyone suggest the solution for this vacuum simulation
> thanks in advance
>
>
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