[gmx-users] Pressure coupling type for Biomembrane simulation

[David van der Spoel]

On Wed, 31 Dec 2003, Yuhua Song wrote:

>Thanks David. For the 6 pressure scaling values needed for xx, yy, zz,
>xy/yx, xz/zx and yz/zy, if xy/yx, xz/zx and yz/zy are set as 0.0, xx, yy, zz
>are set as the same number, Does it has differenec from the iostropic

Yes, the box can expand and contract indepedently in X, y, z, as a 
response to the pressure in x,y,z respectively


>pressure coupling way? Also, for the compressibility, the typical value is:
>4.5e-5 (mostly used that I see in the tutorial etc),  are there some reasons
>for choosing the compressibility in xx, yy, zz as 4e-5 other than 4.5e-5?
yes, the number here is the compressibility of water. May be different for 
other liquids though. On the other hand it is just a factor on the 
coupling time tau_p. Finally, the compressibility of simulated water is 
probably not the same as real water!


>Thanks,
>
>Yuhua
>
>
>
>> >I am doing the biomembrane simulaiton, I am wondering that now the
>experts
>> >in the Biomembrane simulations deal with the pressure coupling type for
>> >Biomembrane simulation. Using pcoupltype as isotropic or anisotropic,
>which
>> >one is more physiological reasonable? Also if choosing the anisotropic,
>what
>> >should be the 6 pressure scaling values needed for xx, yy, zz, xy/yx,
>xz/zx
>> >and yz/zy components respectively.
>> no expeert, but anisotropic
>>
>> compress = 4e-5 4e-5 4e-5 0 0 0
>>
>> the last values prevent your box from becoming skewed.
>>
>> >
>> >Thank you very much in advance.
>> >
>> >Thanks,
>> >
>> >Yuhua
>> >
>> >
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>>
>> -- 
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,  75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
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>
>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++