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production run weak coupling
- siti
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8 years 1 month ago #5396
by siti
production run weak coupling was created by siti
Hi
I would like to run a peptide in DPPC bilayer. Do I need to couple the protein with DPPC for the temperature?
below is part of my md.mdp:
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps = Protein DPPC W
; Time constant (ps) and reference temperature (K)
tau_t = 0.5 0.5 0.5
ref_t = 323 323 323
; pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No
Thank you for your explanation.
Siti
I would like to run a peptide in DPPC bilayer. Do I need to couple the protein with DPPC for the temperature?
below is part of my md.mdp:
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps = Protein DPPC W
; Time constant (ps) and reference temperature (K)
tau_t = 0.5 0.5 0.5
ref_t = 323 323 323
; pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 12.0 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No
Thank you for your explanation.
Siti
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- peterkroon
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8 years 4 weeks ago #5406
by peterkroon
Replied by peterkroon on topic production run weak coupling
This is always a difficult question. What you want is a single temperature distribution for all your particles, but energy transfer from e.g. a membrane to the solvent is often not enough to achieve this -- this is why people use separate temperature coupling groups.
Is your protein embedded in the membrane? If so, I think I would combine the protein and membrane temperature coupling groups (but I'm no expert on membranes). If you do, check the temperature distribution in the protein after your simulation to validate your choice.
Also, be sure to consult www.gromacs.org/Documentation/Terminology/Thermostats .
Is your protein embedded in the membrane? If so, I think I would combine the protein and membrane temperature coupling groups (but I'm no expert on membranes). If you do, check the temperature distribution in the protein after your simulation to validate your choice.
Also, be sure to consult www.gromacs.org/Documentation/Terminology/Thermostats .
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