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 and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: 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.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.htmland another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html. Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. 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. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: 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 http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. 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. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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 and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rasoul nasiri wrote: 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.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. 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. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org
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 force field you can find. As for Go-models, you've already been given advice on that topic: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047496.html -Justin Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: 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 (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: 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 http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. 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. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
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 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 nasiri1...@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 clav...@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 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 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.abra...@anu.edu.auwrote: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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 clav...@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.htmlhttp://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 nasiri1...@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 clav...@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 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 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.abra...@anu.edu.auwrote: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
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 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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.abra...@anu.edu.auwrote: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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.abra...@anu.edu.auwrote: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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 clav...@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 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 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.abra...@anu.edu.auwrote: 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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? The values in vdwradii.dat are not used in the actual simulation. They are used by tools like editconf and genbox when building the system. Attractive and repulsive parameters for nonbonded interactions are defined by the force field, which is assembled in the input to mdrun. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
