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

[rasoul nasiri]

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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