[gmx-users] g_dist with multiple chains of molecules
Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, I want to calculate the distance between C1 and C2 atom in each chain and average over them. I was trying to use gromacs 4.0.7 g_dist tool . For that, I first created two index-groups of all C1 and C2 . But. I realized that g_dist will give me actually the distance between center of mass of all C1 and center of mass of all C2 which is NOT certainly I was looking for. So, I was wondering whether there is any other tool which can split the entire index group by deviding it by total number of chains and then calculate each individual distances for each chain and then do an average over them. An analogous tool exists for g_gyrate where where one can use -nmol option to split the entire index accordingly and calculate the radius of gyration averaged over all the molecules. I was looking for something for calculating distances between two atoms for many chain molecules. I looked at the mailing list but I could not find any solutions for these. Any help will be appreciated. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist with multiple chains of molecules
Sanku M wrote: Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, I want to calculate the distance between C1 and C2 atom in each chain and average over them. I was trying to use gromacs 4.0.7 g_dist tool . For that, I first created two index-groups of all C1 and C2 . But. I realized that g_dist will give me actually the distance between center of mass of all C1 and center of mass of all C2 which is NOT certainly I was looking for. So, I was wondering whether there is any other tool which can split the entire index group by deviding it by total number of chains and then calculate each individual distances for each chain and then do an average over them. You can split the group within make_ndx. There are various splitting keywords (like 'splitat' or 'splitres') that can divide up your index groups. Then script the 100 calls to g_dist. -Justin An analogous tool exists for g_gyrate where where one can use -nmol option to split the entire index accordingly and calculate the radius of gyration averaged over all the molecules. I was looking for something for calculating distances between two atoms for many chain molecules. I looked at the mailing list but I could not find any solutions for these. Any help will be appreciated. Sanku -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist with multiple chains of molecules
On 15/07/2011 6:37 AM, Sanku M wrote: Hi, I am running a simulation where I have 100 chains of molecule in a box . I am trying to calculate the distance between two particular atoms ( present in each molecule) averaged over all the chains of molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, I want to calculate the distance between C1 and C2 atom in each chain and average over them. I was trying to use gromacs 4.0.7 g_dist tool . For that, I first created two index-groups of all C1 and C2 . But. I realized that g_dist will give me actually the distance between center of mass of all C1 and center of mass of all C2 which is NOT certainly I was looking for. So, I was wondering whether there is any other tool which can split the entire index group by deviding it by total number of chains and then calculate each individual distances for each chain and then do an average over them. Check out g_dist -h. There are some other tools suggested there that look at inter-group distances in a different ways, and one of them works well for you. Mark An analogous tool exists for g_gyrate where where one can use -nmol option to split the entire index accordingly and calculate the radius of gyration averaged over all the molecules. I was looking for something for calculating distances between two atoms for many chain molecules. I looked at the mailing list but I could not find any solutions for these. Any help will be appreciated. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
