[gmx-users] Re: genbox generating acetonitrile box with holes

[Vitaly Chaban]

On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz <vedat.durmaz at gmx.net> wrote:
> hi vitaly,
>
> the only acetonitrile boxe that i was able to find is the one provided by
> christoph freudenberger in 2003:
>
> http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz

Maybe somewhere on other old website if they lost it while migrating
to the new one - there should have been a few carbon nanotubes + ACN
systems. If you need a 6-point ACN box, I can find it on my own
archives.

> where exactly is yours? i am simulating with that solvent at the moment but
> the charges are different from the the ones mentioned above .. and the
> density is a little less than it should be (640g/ml).

Hmm... Is 640 kg/m3 the density with protein? What it should be then
(if with protein)?

The density of the bulk ACN is 770kg/m3 at 300K, and the model, which
we used, reproduces it perfectly.

-
Dr. Vitaly V. Chaban



> Am 05.11.2010 19:16, schrieb Vitaly Chaban:
>>
>> Diana -
>>
>> I just wonder how the density of your system behaves while you run NPT
>> equilibration? Do you monitor it? Did you estimate the size of these
>> holes? Maybe they are just due to a visualization utility that uses
>> inappropriate atomic radii?
>>
>> Vitaly
>>
>>
>>
>> On Fri, Nov 5, 2010 at 2:05 PM, dlousa<dlousa at itqb.unl.pt>  wrote:
>>
>>>
>>> Hi Vitaly,
>>>
>>> Thank you very much for your answer.
>>> I have ran my system in the NPT ensemble and what I observed is that the
>>> holes only disappear when the system is at a stable pressure and
>>> temperature and I have no restraints on the protein. During my
>>> initializtion steps, where I have the protein restrained and stabilize
>>> the
>>> temperature and pressure, the holes persist and even increase and I am
>>> afraid this is not very good for the protein.
>>>
>>> As for the acetonitrile parameters I use the ones by Gee and Van
>>> Gunsteren, 2006, Mol Phys,104, 477 but thanks for your tips.
>>>
>>> Diana
>>>
>>> On Fri, 5 Nov 2010 12:59:51 -0400, Vitaly Chaban<vvchaban at gmail.com>
>>> wrote:
>>>
>>>>
>>>> Hey, Diana -
>>>>
>>>> I believe these acetonitrile holes are not a problem. Just perform an
>>>> equilibration run in the NPT ensemble and they will disappear. The
>>>> more tricky way is to adjust VDW radii in vdwradii.dat before using
>>>> genbox.
>>>>
>>>> By the way, what force field model of acetonitrile do you use here?
>>>> Some time ago I uploaded a few simulation boxes with acetonitrile onto
>>>> the gromacs official website, hopefully they can be also useful for
>>>> you to start.
>>>>
>>>> Good luck!
>>>>
>>>> Dr. Vitaly V. Chaban         |  skype: vvchaban
>>>> Department of Chemistry      |  email: v.chaban at rochester.edu
>>>> University of Rochester      |  email: vvchaban at gmail.com
>>>> Rochester, NY 14627-0216     |  email: chaban at univer.kharkov.ua
>>>> United States of America     |  WWW:
>>>> chem.rochester.edu/~prezhdo_group/index.php/members/5-vitaly-chaban
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>> I am trying to solvate a protein in a box of acetonitrile using genbox.
>>>>> My
>>>>> initial solvent box is a cubic box containing 300 molecules of
>>>>> acetonitrile
>>>>> that has been equilibrated for 500 ps at constant P and T.
>>>>>
>>>>> I used the following protocol to generate the box:
>>>>>
>>>>>
>>>
>>>
>>> #######################################################################################
>>>
>>>>>
>>>>> #create the box
>>>>> editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb  -bt dodecahedron
>>>>>
>>>>> #solvate
>>>>> genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o
>>>>> protein_in_acetonitrile.gro
>>>>>
>>>>> #convert the box to visualize it
>>>>> touch empty.mdp
>>>>>
>>>>> grompp -f empty.mdp  -c protein_in_acetonitrile.gro  -p
>>>>> 01_make_top/protein_ACN.top
>>>>> trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb
>>>>> -pbc
>>>>> atom   -ur compact<<EOF
>>>>> 0
>>>>> EOF
>>>>>
>>>>>
>>>
>>>
>>> #######################################################################################
>>>
>>>>>
>>>>> After these steps I get a box that has holes and I can't understand
>>>>>  why.
>>>>>
>>>>> I couldn't send the final pdb file in attachment, if anyone thinks
>>>>>
>>>
>>> he/she
>>>
>>>>>
>>>>> can help and whishes to see the pdb file I will send it to your email.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Diana
>>>>>
>>>>> --
>>>>> Diana Lousa
>>>>> PhD student
>>>>> Protein Modeling Laboratory
>>>>> ITQB/UNL
>>>>> Oeiras, Portugal
>>>>>
>>>
>>>
>
>