[gmx-users] Re: MD with RMSD restraint

the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users

[gmx-users] Re: MD with RMSD restraint

distance deviations, i.e. distance-based RMSD as you suggest. Maybe I can use the averaging over multiple pairs facility, If I change the averaging function (power 2 instead of 6) ? Thanks again, Sam Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I

[gmx-users] MD with RMSD restraint

Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? If yes, could you explain how to do it? If no, what would be the easiest way to implement this in

[gmx-users] error using generic kernel

Dear gmx developers, I'm trying to use the generic kernel with gromacs 4.0.3, by setting the environment variable GMX_NB_GENERIC. However, I get a segmentation fault. Looking at the source code in do_nonbonded(), I found that the function (*kernelptr)() is called regardless if kernelptr ==

[gmx-users] temperature too high with reaction field

Hi gmx users, I'm trying to simulate a water box filled with TIP3P water. With PME, everything seems OK. However, when I switch to reaction field electrostatics, the temperature in the output files is too high: 312K instead of 300K (the t_ref value for the whole system). Maybe there is

[gmx-users] example lookup tables

Hi, The example lookup tables in the directory share/top, table6-8.xvg table6-9.xvg table6-10.xvg table6-11.xvg table6-12.xvg, are all identical. So, which of the vdw potentials is tabulated here? Thanks, Sam Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm