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

Tue Dec 11 10:26:51 CET 2012

I have not followed the thread but concerning the solvation of a  
protein using genbox you need to:
1- use a box of water that has the exact size of the final box you  
want (you make it yourself using any tool you want) and you need to  
define the box size of the protein file as the one of the water box  
conformation. This is given on the last line of the gro file. Then  
genbox -cp -cs should work fine.
2- you need to use a water box size larger than the one you need. This  
solution is generally easier. You can generate a box using genconf - 
nbox option. And again define the box size in the protein conformation  
file and genbox will just do fine.

We generally use -vdwd 0.18. It is a good compromise for disturbing  
the system the least.

Note that these uses have been discussed on the MARTINI forum several  
times.

XAvier.

On Dec 11, 2012, at 9:05 AM, francesco oteri wrote:

> Tanks to all for your advices,
> I am going to check all the different aspect you suggested and I will
> report the results as soon as possible.
>
> Francesco
>
>
> 2012/12/11 Tsjerk Wassenaar <tsjerkw at gmail.com>
>
>> Hi,
>>
>> Visualization is the key. If you check the structure right after  
>> genbox,
>> you should be able to notice something odd. Apparently genbox has a  
>> problem
>> with martini water, which probably means there is a problem with  
>> monoatomic
>> solvents. The problem has been noted before, b ut I'm a bit too  
>> lazy now to
>> check whether it was here or on the martini forum. Using a small  
>> box with a
>> single water molecule for filling will solve the problem.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham <mark.j.abraham at gmail.com
>>> wrote:
>>
>>> On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul <jalemkul at vt.edu>  
>>> wrote:
>>>
>>>>
>>>>
>>>> On 12/10/12 5:45 PM, francesco oteri wrote:
>>>>
>>>>> For Justin,
>>>>> I need this water for one simple reason: less then 20nm doesn't
>>> work....As
>>>>> I said before
>>>>>
>>>>>
>>>> It seems you have identified the source of the problem, and it is
>>>> independent of box size.  I questioned the box size because it  
>>>> seemed
>>>> rather random and you had not shown any data for box sizes less  
>>>> than 19
>>> nm,
>>>> so I was curious how you arrived at the need for 20 nm, more than
>> double
>>>> the size of your solute.
>>>>
>>>> It would be interesting to see if you could identify a minimum  
>>>> box size
>>>> that does not require large numbers of solvent configurations to be
>>> stacked
>>>> within the unit cell.  The only reason I could see for what you're
>>>> reporting is if neighboring solvent blocks somehow get crossed to
>> produce
>>>> overlap when they should simply be next to one another.  The  
>>>> larger the
>>>> box, the greater the probability that this happens.
>>>
>>>
>>> Yeah, that's probably it. The water box has many waters with x
>> coordinates
>>> down at 0.000 and near 10.901, with an x size of 10.902. So  
>>> different box
>>> sizes will randomly introduce unstable water configurations  
>>> according to
>>> whether stuff is too close. This water box is probably not suited  
>>> to the
>>> purpose - its "box size" might not include the half VDW radii  
>>> outside the
>>> water coordinates needed to pack stably.
>>>
>>> Mark
>>>
>>>
>>>>
>>>>
>>>>> 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.
>>>>>>
>>>>>>
>>>>>>
>>>> It is highly unusual for genbox to produce overlapping waters,  
>>>> but per
>>> the
>>>> help description, only solute-solvent overlaps are checked, not
>>>> solvent-solvent, which would likely require enormous amounts of  
>>>> memory
>>> (and
>>>> genbox already has memory issues).
>>>>
>>>> -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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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Biocomputing Group
>> Department of Biological Sciences
>> 2500 University Drive NW
>> Calgary, AB T2N 1N4
>> Canada
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>
>
>
> -- 
> Cordiali saluti, Dr.Oteri Francesco
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