[gmx-users] How can I reconstruct the system in CGMD simulation?

[César Ávila]

For a detailed description of how to set up protein simulation, I recomend
you to read the Martini Tutorial on
http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html
there you will find  step by step instructions along with some explanations
of what you are actually doing.
In this case you only want to build a water box around your protein. For
that you will use editconf and a vdw distance of 0.19.

Regards
Cesar

2009/12/17 rasoul nasiri <nasiri1355 at gmail.com>

> yes, I know there will be limitation for modeling of Folding/Unfolding
> proteins with MARtini CGFF if I want to look at complete folding/unfolding
> mechanism of proteins but I want to find out localized regions of the
> protein (e.g. the C- or N-termini) that they have contribution to the
> denaturation mechanism.
> My question is about vdwd in beads of water. Is it OK if I select distances
> of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to
> reconstruct the system in smaller vdw distance of the water beads for doing
> my purpose. and Which commands of Gromacs can do it?
>
> Best regards
> Rasoul
>
> On Thu, Dec 17, 2009 at 5:03 PM, César Ávila <clavila at gmail.com> wrote:
>
>> I suggest you read the original paper for Martini Protein FF. I think it
>> is not suitable for your purpouse.
>>
>> 2009/12/17 rasoul nasiri <nasiri1355 at gmail.com>
>>
>>> Hi,
>>>
>>> My purpose is finding of denaturation mechanism of proteins with MArtini
>>> CGFF by Gromacs.
>>> I mean after filling box in which there are beads of protein from water
>>> beads with suitable van der wall distance (larger than 0.105nm), when I want
>>> to start production phase, first switch back to the smaller radius of van
>>> der waals of the water beads, then I will continue CGMD simulation. Is it
>>> possible I reduce this radius? Which commands of Gromacs suit can do it?
>>>
>>> Rasoul
>>>
>>>
>>> On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>>>
>>>> rasoul nasiri wrote:
>>>>
>>>>> greetings GMX users,
>>>>>
>>>>> When I use genbox command for filling solvent in CGMD simulation with
>>>>> Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
>>>>> when I use default value (0.105nm), system will crash. Which distance is
>>>>> suitable for performing CGMD simulation. I used  0.15 or 0.2nm as distances.
>>>>> Are those OK?
>>>>>
>>>>
>>>> Read up on your forcefield and find out how "large" the particles tend
>>>> to be. It only has to be good enough, not perfect.
>>>>
>>>>
>>>>  I have to switch back to the smaller radius afterward, Is it correct?
>>>>>
>>>>
>>>> Changing what for what purpose?
>>>>
>>>>
>>>>  if yes, How can I do it? I tried with editconf but could not.
>>>>>
>>>>
>>>> I don't know what you mean.
>>>>
>>>> Mark
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