[gmx-users] semi isotropic settings

[Justin Lemkul]

On 3/30/13 11:47 AM, Elisabeth wrote:
> Hi Justin,
>
> The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two.

No, it is not a ratio.  The use of "x/y" simply means both x and y.

> If thats nto the case I guess compressibility     = 3.5e-5  0 is the
> correct value. What do you think?
>

Sounds more reasonable.

-Justin

> On 30 March 2013 11:41, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/30/13 11:39 AM, Elisabeth wrote:
>>
>>> Hi all,
>>>
>>> I wanted to use Pcoupltype          =  semiisotropic    but I am not clear
>>> about the compressibility settings if I want to keep Z directions fixed in
>>> my system and letting X and Y change. Which case 1 or 2 is correct for
>>> semi
>>> isotropic option?
>>>
>>> 1) compressibility     =  3.5e-5 3.5e-5 0
>>>
>>> 2 ) or compressibility     =  1 0?
>>> Manual says 2 values are needed for x/y and z directions respectively.
>>>
>>>
>> Case #2, though I doubt a value of 1 is a correct compressibility.  But as
>> the manual says, you need two values - one for x/y (i.e. those two
>> dimensions are equally compressible) and one for z.
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================