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
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
> Hi,
>
> Visualization is the key. If you check the structure right after genbox,
> you should be able to notice s
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
On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul 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 workAs
>> I said before
>>
>>
> It seems you have identified the source of the problem, and it is
> inde
On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri wrote:
> 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.
>
Don't change things until you know *why* t
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 workAs
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 ran
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
2012/12/10 francesco oteri
> 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
>
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 super
On Mon, Dec 10, 2012 at 11:15 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
> mi
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 th
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
On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
wrote:
> Dear gromacs users,
>
> I am facing a very tricky problem in building a stable topology.
> In particular I am trying to use MARTINI force-field and I noticed that if
> I use a box whose the side size is smaller than 20nm, the minimization
>
On 12/10/12 3:48 PM, francesco oteri wrote:
Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than 20nm, the minimization
fails with this mes
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