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

[César Ávila]

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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>
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