[gmx-users] how choose k value in .ppa file

Hi, gromacs users I've a little question about the pulling procedure at constant rate. I defined pull and reference group both constituted by 18 atoms. My problem is to define the spring value in .ppa file. Given that my groups have N atoms, how do I choose a suitable spring value quantitative

[gmx-users] ffG43a1.n2t

Dear all,I ran x2top (gromacs 3.3) command to get DNA.top file from DNA.gro. But it gave me error for all the forcefields I used. The error was as follows:Fatal error: Library file ffG43a1.n2t not found in current dir nor in default directories.Also when I used other forcefields it gave me s

[gmx-users] Problem with DNA chain

otide monomers. For instance, in the ATC sequence the bond term between A-T and between T-C are missing. I would need some help in order to understand if it is necessary to modify the Termini Database (ffG43a1-c.tdb,ffG43a1-n.tdb) or something else. Thank you. Best regards, Marco