Tot Ziens!
Op 4 mar 2012 om 18:44 heeft "Andrew DeYoung" <[email protected]> het volgende geschreven: > Hi, > > If you have time, I would be grateful for any advice you have about which > structure file format that I should use. I am attempting to create a carbon > nanotube. However, the carbon-carbon bond length that I would like to use > is 0.1415 nm, which means that I would like a structure file format that can > take positions up to accuracies of at least 0.0001 nm. > > Unfortunately, the .gro file format only accepts positions up to accuracies > of 0.001 nm. This means that if I use .gro, I will need to round the > carbon-carbon bond length to 0.142 nm or 0.141 nm, which I would prefer not > to do. > > Now, I know that the Gromacs code itself uses many more decimal places > internally for running MD (single precision give a lot of decimal places and > double precision gives even more). I think this means that if I specify the > carbon-carbon bond length in my topology as 0.1415 nm in [ bonds ] (and the > .itp file format, and others, allow this type of precision) then even if I > must use 0.142 nm in my starting configuration .gro file, the bond lengths > will equilibrate to ~0.1415 nm if I run a short simulation (given that the > Gromacs code internally uses high precision). > > Yet, what if I need my starting configuration to have high precision bond > lengths (0.1415 nm)? I plan to freeze the carbon atoms using a freeze > group, and it would be easiest if I could do this from the get-go (i.e., > without running equilibration in which the carbon atoms are unfrozen). > > Do you have any advice about which file format I should use? I need not be > "constrained" by .gro > (http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_ne > ed_for_a_.gro_file). > G96 > .pdb, it seems > (http://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)#Example), > gives position precision up to 0.001 ANGSTROM (or 0.0001 nm), which means > .pdb will give me just enough precision. Or should I instead write my > starting configuration in a .g96 file, which allows very high position > precision? However, other than > http://manual.gromacs.org/current/online/g96.html, I am having some > difficulty (even with Google) locating detailed information about the .g96 > file format. Unfortunately, my institution I do not think has a GROMOS-96 > license, so I cannot access its manual. > > Between .pdb and .g96, which would you recommend? Or is there any other > structure file format that I am not thinking of? > > Thanks so much. > > Andrew DeYoung > Carnegie Mellon University > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
