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-rdd option error
- dave
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9 years 1 month ago #4493
by dave
-rdd option error was created by dave
Hi,
I am simulating membrane with peptide and I usually get this error though restarting job completes nicely. I am not sure what is causing this and How to resolve this. It says I should set -rdd option but what value I should use. (how to decide?)
Error:
7 of the 13326 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
Here is my mdp file:
dt = 0.02
nsteps = 50000000
nstxout = 0
nstvout = 0
nstlog = 10000
nstxtcout = 1000
xtc-precision = 100
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = PEPTIDE POPC W_NA
tau-t = 1.0 1.0 1.0
ref-t = 300 300 300
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau-p = 12.0 12.0
compressibility = 3e-4 3e-4
ref-p = 1.0 1.0
continuation = yes
gen_vel = no
I am simulating membrane with peptide and I usually get this error though restarting job completes nicely. I am not sure what is causing this and How to resolve this. It says I should set -rdd option but what value I should use. (how to decide?)
Error:
7 of the 13326 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
Here is my mdp file:
dt = 0.02
nsteps = 50000000
nstxout = 0
nstvout = 0
nstlog = 10000
nstxtcout = 1000
xtc-precision = 100
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = PEPTIDE POPC W_NA
tau-t = 1.0 1.0 1.0
ref-t = 300 300 300
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau-p = 12.0 12.0
compressibility = 3e-4 3e-4
ref-p = 1.0 1.0
continuation = yes
gen_vel = no
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- floris
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- Posts: 15
9 years 3 weeks ago #4504
by floris
Replied by floris on topic -rdd option error
try 1.6, if this does not work, you can increase to 1.8
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