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protein-linc warning!
- yamahdi
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13 years 4 months ago #455
by yamahdi
protein-linc warning! was created by yamahdi
Hi
I have try to simulate some proteins but all of them failed in short minimization(in vaccum) step! I also change the maximum durable force from 1000 t0 100 for toypeptide and the problem was saw also there! the warning is LINC warning(bond and angle rotation).
would you please help me explaining where may be my mistake?
thanks
I have try to simulate some proteins but all of them failed in short minimization(in vaccum) step! I also change the maximum durable force from 1000 t0 100 for toypeptide and the problem was saw also there! the warning is LINC warning(bond and angle rotation).
would you please help me explaining where may be my mistake?
thanks
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- richor
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10 years 5 months ago #2970
by richor
Replied by richor on topic protein-linc warning!
All Maritini users:
I have the same problem too,though not so seriously.
Lincs warning will occur in my system after hundreds of ns simulation.
There may be two reason here: i. The protein I parametered using Martinize.py have some residues in unfavorable position.
ii.The mdp parameter for the protein is not appropriate.
I put my mdp parameter here:
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = PME
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein POPE_POPG PW_ION
tau_t = 1.0 1.0 1.0
ref_t = 320 320 320
Pcoupl = Berendsen
Pcoupltype = semiisotropic
;tau_p = 1.0 1.0
tau_p = 3.0 3.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
refcoord_scaling = com
If the problem is the first one,how can I repair that? After all,we cannot make sure the itp and gro file generated by martinize.py can be ran without LINCS warning.
I have the same problem too,though not so seriously.
Lincs warning will occur in my system after hundreds of ns simulation.
There may be two reason here: i. The protein I parametered using Martinize.py have some residues in unfavorable position.
ii.The mdp parameter for the protein is not appropriate.
I put my mdp parameter here:
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = PME
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein POPE_POPG PW_ION
tau_t = 1.0 1.0 1.0
ref_t = 320 320 320
Pcoupl = Berendsen
Pcoupltype = semiisotropic
;tau_p = 1.0 1.0
tau_p = 3.0 3.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
refcoord_scaling = com
If the problem is the first one,how can I repair that? After all,we cannot make sure the itp and gro file generated by martinize.py can be ran without LINCS warning.
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