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

Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet

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

rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information

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

Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Justin, Thank you for your

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

rasoul nasiri wrote: Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? There are several CG models out there, but I don't know much about them. The nice thing about Gromacs is that it can use any

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

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

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

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

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

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

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

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

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

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

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

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 nasiri1...@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

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

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

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

rasoul nasiri wrote: 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