Re: [gmx-users] Bound water calculation (Justin Lemukel)
Hello, I want to calculate the number of water molecules participating in inter chain hydrogen bonds between multiple chains that are associating in concentrated aqueous solution. My system contains multiple polymer chains, water molecules and counterions. I also want to calculate the bound water content for my above system. How to do this using GROMACS ? Please suggest. I'm using GROMACS 4.0.7 for my study. Regards -- Abhishek -- 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] Finding Average Net charge as a function of distance from a polymer segment
Dear Gromacs Users I want to examine the distribution of counterions in my system at larger length scales comparable to the size of the molecule. I have used RDF's to find the distribution of ions till half the box size. Can I consider half the box size as larger length scale ? I have found in a paper that ion distribution surrounding the polymer can be calculated without normalizing by the volume of the spherical shell via average net charge calculation for diffuse counterions in my system. My question is How can I find the average net charge as a function of distance from the polymer segement for a polymer chain using GROMACS 4.0.7 ? My system contains a single polymer chain, counterions and mixed solvent. I will be grateful for the solution of the above issue. Regards -- Abhishek Kumar Gupta Research Scholar -- 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] Finding the distribution of counterions around the polymer (polyelectrolyte) at larger scales
Dear all, I have used the radial distribution functions to examine the structure and distribution of ions in the proximity of the polyelectrolyte and studied the spation distribution of ions at the smallest length scales. I have to now examine the distribution of counterions at larger scale as well, that is at length scale comparable to the size of the molecule. How i can find the distribution of counterions in my system at larger scale as well ?. I have used GROMACS 4.0.7 for my simulation study of a single polyelectrolyte chain in aqueous solutions of alcohol in presence of counterions. Please help Regards Abhishek -- Abhishek Kumar Gupta Research Scholar Macromolecular modeling and Simulation Lab Chemical Engineering Dept. IIT Madras, Chennai-600036 India -- 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] Unable to visualize my Polymer chains in VMD software generated using RIS theory in a proper way
Dear GROMACS Users, I am trying to visualize the simple polyethylene chains (multiple chains) consisting of certain number of atoms generated using RIS theory using VMD. I'm using the PDB format to express coordinates to visualize my chains. The chains are very random and at some points multiple atoms of a chain comes very near to each other. Sometimes, even there is inter chain overlapping and multiple atoms of different chains comes in close vicinity of each other. In such a situation, while visualizing via. VMD, there appears a bond between those close or very close atoms within a chain or between two chains. Therefore, the visulaization by VMD shows that number of bonds is much greater than the number of atoms and forms a cage like structure (in some cases) between the closely spaced or overlapping atoms. What might be the possible cause of this ? Does VMD connects Atoms taking in some distance criterion ? Can we change that distance criteria that VMD utilize to connect the atoms of a polymer chain in succession ? Thanks and Regards-- Abhishek -- 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.
