[gmx-users] free energy caculation error

[Szilárd Páll]

lmgtfy: http://bit.ly/1lJYVGQ ;)
--
Szilárd


On Wed, Apr 9, 2014 at 12:41 PM, jane <348363213 at qq.com> wrote:
> Hi all,
> I want to caculate the free energy of a molecule, but when I run the MD, it
> appears the error: "There is no domain decomposition for 8 nodes that is
> compatible with the given box and a minimum cell size of 4.44444 nm. Change
> the number of nodes or mdrun option -rdd or -dds".However, even though i
> added the -rdd and -dds, the error is same as the previous. my mdp file as
> follows.
>
> ; we'll use the sd integrator
> ;run parameters
> integrator          =  sd
> dt                  =  0.002                       ; ps
> nsteps              =  5000                    ; total 1ns
> nstcomm             =  100
>
> ; turn off trajectory writing
> nstxout                  = 0
> nstvout                  = 0
> ; cut-offs at 1nm
> rlist                    = 1.0
> nstlist                  = 10
> coulombtype              = pme
> vdw-type                 = cut-off
> rvdw                     = 1.0
> constraints              = all-bonds
> ; set temperature to 300K
> tcoupl                   = v-rescale
> tc-grps                  = system
> tau-t                    = 0.2
> ref-t                    = 300
> ; and pressure to 1 bar
> pcoupl                   = parrinello-rahman
> ref-p                          = 1
> compressibility          = 4.5e-5
> tau-p                          = 5
> ; and set the free energy parameters
> free-energy              = yes
> couple-moltype           = RNA_chain_A
> init-lambda              = 0
> ; these 'soft-core' parameters make sure we never get overlapping
> ; charges as lambda goes to 0
> sc-power                 = 1
> sc-sigma                 = 0.3
> sc-alpha                 = 1.0
> ; we still want the molecule to interact with itself at lambda=0
> couple-intramol          = no
> couple-lambda1           = vdwq
> couple-lambda0           = none
> foreign-lambda           = 0 0.2 0.4 0.6 0.8 0.9 1
> nstdhdl                  = 10
> separate-dhdl-file       = yes
> dhdl-derivatives         = yes
> dh_hist_size             = 5
> dh_hist_spacing          = 50
>
> thanks for advances.
>
>
> --
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