[gmx-users] Error with MARTINI depending by the box size

[francesco oteri]

For Justin,
I need this water for one simple reason: less then 20nm doesn't work....As
I said before


2012/12/10 francesco oteri <francesco.oteri at gmail.com>

> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>
> Looking carefully at the configurations, I found that the water molecule
> originating the error is exactly superimposed to an other molecule so I
> simply deleted it and the same error is reported for an other water
> molecule.
>
> Although I could scan all the pdb to detect all the superimposed water
> molecules, I believed genbox checked for this. Of course the original box
> does't contain superimposed molecules.
>
>
> Francesco
>
>
> 2012/12/10 Justin Lemkul <jalemkul at vt.edu>
>
>>
>>
>> On 12/10/12 5:15 PM, francesco oteri wrote:
>>
>>> Actually, since I copied and pasted the mail, there is an imprecision.
>>> When
>>> I use 20nm as box side lenght I don't get
>>> any error, everything goes fine.
>>>
>>> I actually tested different size between 19 and 20 nm and I found that
>>> the
>>> minimum size to avoid the error is 19.5nm.
>>> My system has an average size and, as stated by vmd, it size are
>>> X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
>>> So a box of 20nm, as well as 19nm, is large enough to accomodate the
>>> protein.
>>>
>>>
>> Those box sizes are vast overkill.  Any reason why you need so much extra
>> water?
>>
>>
>>  Moreover, since I remove the water around the protein (that is already
>>> stabie because of the in vacuo minimization), the problem has to be in
>>> the
>>> bulk water!
>>>
>>>
>> As I said before, you should be able to identify the source of the
>> problem by simple visualization based on what mdrun has told you.
>>
>>
>> -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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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco