Rebeca García Fandiño wrote:
Hello,
I am new in Gromacs, and I am trying to simulate the interaction between
a DOPC membrane and a protein.
I have equilibrated my system at constant volume and now I would like to
switch to constant pressure.
I think the best option for me is to use ANISOTROPIC pressure, because I
want to study the ondulations produced in the membrane due to the
protein. Do you recommend anisotropic pressure for this? or
semiisotropic would be enough?
A good discussion of such topics can be found in: Kandt, et al. (2007) Methods
41: 475-488.
Another question is about the values of tau_p and ref_p. I have read in
the manual that in the case of anisotropic pressure I should use 6
values. Which values do you recommend to use? Should I use also 6 values
for compressibility and ref_p?
Pcoupl = Berendsen
Pcoupltype = anisotropic
tau_p = 2.0 2.0 2.0 2.0 2.0 2.0
Only one value of tau_p is necessary.
compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
Setting the off-diagonal compressibilities as such may lead to deformations of
the box. From the manual:
"When the off-diagonal compressibilities are set to zero, a rectangular box will
stay rectangular. Beware that anisotropic scaling can lead to extreme
deformation of the simulation box."
ref_p = 1.0 1.0 1.0 1.0 1.0 1.0
Similarly, you are specifying a pressure in the diagonal directions (the last
three values).
-Justin
Thank you very much for your help in advance.
Best wishes,
Rebeca García Fandiño
Parc Cientific de Barcelona
[EMAIL PROTECTED]
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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