[gmx-users] free energy caculation error

[jane]

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.


--
View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.