[gmx-users] make_ndx and rdf
Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file ? Carbon in group 1 hydrogen in group 2 oxygen in group 2 group 2 is water I will be gratefull for your helps. All the best.-- 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
[gmx-users] gromacs 4.5.4 analysis tools
Dear gmx users, I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD output files. I have some NAMD output files : output.coor , output.vel , output.dcd (binary coordinate trajectory output file). Can I convert these output files into gromacs output files and use gromacs 4.5.4 analysis tools ? If it’s possible to do it, could you please explain this job ? Thanks in advanceM-- 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] using more than one type of molecules
Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ? Sincerely From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, March 13, 2009 8:25:14 PM Subject: Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: > > > Dear All, > > > I'm new to Gromacs and have some questions to learn the answers. I study on > one type molecule. If I want to add lets say 240 molecules, which is the best > way to use editconf or genbox ? And I learned the procedure of using more > than one type of molecules in gromacs. But I'm not sure, so I'm waiting for > your contributions. Assume that I have two small organic In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule. Use editconf to set your box size, and genbox -ci -nmol to insert what you need. > molecules like hydrocarbons X and Y. I think First I will have to get > seperately DRGGMX.ITP and DRGPOH..PDB for the each molecules in different If these come from PRODRG, they will probably require manual modification and validation of their contents. > work directories. Then chose one directory ( X ) and do the operations like > in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command > > > genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top > > If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water). > After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the > number of Y molecule and go on .. > Correct. -Justin > > Could you please help me to learn the true process of using more than one > type of molecules in gromacs ? > > > > Sincerely > > > > > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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 list gmx-users@gromacs.org http://www.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://www.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] using more than one type of molecules
Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecules in gromacs. But I'm not sure, so I'm waiting for your contributions. Assume that I have two small organic molecules like hydrocarbons X and Y. I think First I will have to get seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in different work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of Y molecule and go on .. Could you please help me to learn the true process of using more than one type of molecules in gromacs ? Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] n-alkanes simulations in Gromacs
Dear Gromacs Users, I’m interested in n-alkanes and evaluating thermophysical and structural properties of n- alkanes and binary mixtures of n-alkanes. I want to use Gromacs and the force fields in Gromacs for my n-alkanes simulations. And I want to ask some questions to you. First, I’m planning to generate a packmol pdb file that includes 100 molecules for pure and binary mixtures. Can I directly use this pdb file with pdb2gmx ? Can I use the partial charges generated with Gaussian for n-alkanes molecules ? If so, what is the procedure of this ? How can I load the partial charges into Gromacs ? And Finally, I want to use both all atom and United atom force fields. Could you suggest me some force fields that can be used for n-alkanes md simulations ? Thanks in advance Kind regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
