[gmx-users] Error with MARTINI depending by the box size
francesco.oteri at gmail.com
Mon Dec 10 23:45:48 CET 2012
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
> 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.
> 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.
>>> 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
>>> 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
>> Those box sizes are vast overkill. Any reason why you need so much extra
>> 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
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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> Cordiali saluti, Dr.Oteri Francesco
Cordiali saluti, Dr.Oteri Francesco
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