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

francesco oteri francesco.oteri at gmail.com
Mon Dec 10 23:44:39 CET 2012

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.
>> 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>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

Cordiali saluti, Dr.Oteri Francesco

More information about the gromacs.org_gmx-users mailing list