Hello, This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem.
As water is present in the system, so according to the manual the define in the .mdp file must be -DFLEXIBLE. No probem in that. But I read in different works by other people that for DNA they are using NPT ensemble. But there are two couplings in the .mdp file. 1. temparature coupling 2. Pressure coupling I want to ask that which coupling will be better for temperature; a. Berendsen coupling b. V-rescale coupling c. nose-hoover coupling AND for pressure: a. Berendsen coupling b. Parrinello-Rahman coupling c. Martyna-Tuckerman-Tobias-Klein implementation coupling I am also little confused over the pcoupltype, where options are isotropic; semi-isotropic and anisotropic. Please help me in this matter. Thanks in advance; ======================================================== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] ======================================================== -- gmx-users mailing list gmx-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