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

[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
>