[gmx-users] free energy caculation error
jane
348363213 at qq.com
Wed Apr 9 12:42:32 CEST 2014
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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