Re: [gmx-users] CG MD
Backwards is one such tool http://pubs.acs.org/doi/abs/10.1021/ct400617g http://cgmartini.nl/index.php/tools2/resolution-transformation Peter On 26-06-17 18:01, Alex Mathew wrote: >> though most atomistic properties can be studied by rebuilding the > atomistic coordinates from the CG. Various methods exist to >do this. > > Could you please provide a link to any material or paper for this. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG MD
>though most atomistic properties can be studied by rebuilding the atomistic coordinates from the CG. Various methods exist to >do this. Could you please provide a link to any material or paper for this. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG MD
On 6/23/17 10:26 AM, Alex Mathew wrote: Dear all, I was wondering the analysis we usually use in the all-atom simulation will work in for CG model? I guess secondary structural analysis will be useless since it's not considering all atoms. What about non-bonded energies and other parameters such hydrogen bond and essential dynamics? What do people do in the literature to address the same types of questions you're asking. H-bonding is a microscopic property and likely is not going to be addressed via CG, though most atomistic properties can be studied by rebuilding the atomistic coordinates from the CG. Various methods exist to do this. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CG MD
Dear all, I was wondering the analysis we usually use in the all-atom simulation will work in for CG model? I guess secondary structural analysis will be useless since it's not considering all atoms. What about non-bonded energies and other parameters such hydrogen bond and essential dynamics? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Dear Gromacs Users, I have a insilico model of Mycobacterium cell wall (surface) protein which has no transmembrane helices.Which Gromacs tutorials should I follow for MD studies to know about its conformational stability and latter for protein - ligand studies. Kindly guide me Thanking you with regards V.G.Shanmuga Priya On Mon, Dec 26, 2016 at 11:06 PM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > Hi Quyen, > > Although Martini is a good CG force field for a system contains lipids and > proteins, it still needs some improvements to capture conformational > changes (especially large changes). > Is there any hybrid model available (and ready to use) for such a system? > > > Regards, > Dariush > > On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu wrote: > > > Nikhil say: > > > > I would like to study the conformational study of proteins (Amyloid beta) > > in presence of lipid bilayers and other molecules. Can anyone tell me the > > possibility of Coarse-grained molecular dynamics for this study, since > > all-atom MD need more time and my system contains more atoms, so I'm > > thinking to go for CGMD. in CG-MD can we do the same analysis as in > > All-atom MD.? > > > > > > You need to find a force field that support for protein coarse-grain > model > > > > such as Martini: http://cgmartini.nl/ > > > > to save simulation time you can you CG model or hybrid model( result > > better than CG model because a important region > > > > is treated as standard MD, less important region is use CG model > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Hi Quyen, Although Martini is a good CG force field for a system contains lipids and proteins, it still needs some improvements to capture conformational changes (especially large changes). Is there any hybrid model available (and ready to use) for such a system? Regards, Dariush On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu wrote: > Nikhil say: > > I would like to study the conformational study of proteins (Amyloid beta) > in presence of lipid bilayers and other molecules. Can anyone tell me the > possibility of Coarse-grained molecular dynamics for this study, since > all-atom MD need more time and my system contains more atoms, so I'm > thinking to go for CGMD. in CG-MD can we do the same analysis as in > All-atom MD.? > > > You need to find a force field that support for protein coarse-grain model > > such as Martini: http://cgmartini.nl/ > > to save simulation time you can you CG model or hybrid model( result > better than CG model because a important region > > is treated as standard MD, less important region is use CG model > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Nikhil say: I would like to study the conformational study of proteins (Amyloid beta) in presence of lipid bilayers and other molecules. Can anyone tell me the possibility of Coarse-grained molecular dynamics for this study, since all-atom MD need more time and my system contains more atoms, so I'm thinking to go for CGMD. in CG-MD can we do the same analysis as in All-atom MD.? You need to find a force field that support for protein coarse-grain model such as Martini: http://cgmartini.nl/ to save simulation time you can you CG model or hybrid model( result better than CG model because a important region is treated as standard MD, less important region is use CG model -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CG-MD to study the conformational changes of proteins...
I would like to study the conformational study of proteins (Amyloid beta) in presence of lipid bilayers and other molecules. Can anyone tell me the possibility of Coarse-grained molecular dynamics for this study, since all-atom MD need more time and my system contains more atoms, so I'm thinking to go for CGMD. in CG-MD can we do the same analysis as in All-atom MD.? -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CG MD Simulation of DNA and PAMAM dendrimers
Hi. This mail list can not take attachment. So it might be better to just past the mdp file in the message. At which time step did the segmentation fault happen? On Wed, Dec 17, 2014 at 1:43 PM, Doa Hawamdeh wrote: > > Dear GROMACS users: > > I want to study the complexation between PAMAM dendrimer and DNA using > coarse-graining molecular dynamics simualtions (MARTINI force field) > utilizing GROMACS version 5.0.3. > > MD integrator is used with time step of 20 fs, but I could not run the > simulation with this time step, I got *segmentation fault. *Sure before > running long simulation I minimized the system. I attached the .mdp file > that I use. Could you please help me? > > Waiting your response. > > Thank you. > Doa > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CG MD Simulation of DNA and PAMAM dendrimers
Dear GROMACS users: I want to study the complexation between PAMAM dendrimer and DNA using coarse-graining molecular dynamics simualtions (MARTINI force field) utilizing GROMACS version 5.0.3. MD integrator is used with time step of 20 fs, but I could not run the simulation with this time step, I got *segmentation fault. *Sure before running long simulation I minimized the system. I attached the .mdp file that I use. Could you please help me? Waiting your response. Thank you. Doa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
