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

[rasoul nasiri]

Dear Cesar,
Thank you for your reply,

There are two different kind of water gro in this site (one of them is
water.gro in :
http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
and another is water-1bar-303k.gro in :
 http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there difference
between them?
Can I build water.gro with coarse graining beads (P4) from spc216.gro with
using atom2cg.awk script?

Another question; How can I change secondary structure information during
CGMD simulation, If I want to perform CGMD simulation for finding of the
folding/unfolding mechanism in proteins completely? Because Martini CGFF
consider fix it.

Cheers
Rasoul


On Fri, Dec 18, 2009 at 9:02 PM, César Ávila <clavila at gmail.com> wrote:

> For a detailed description of how to set up protein simulation, I recommend
> you to read the Martini Tutorial on
> http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html<http://md.chem.rug.nl/%7Emarrink/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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