[gmx-users] shift functions in gromacs

Hello everyone, I'd like to ask for some clarification of actual form of shift fuctions used in gromacs. Due to gromacs tutorial 4.5.4 (section 4.1.5) and equations 4.23, 4.26-4.31 shift fuction seems to depend only on 2 user-defined conctants - r1 and rc which seems to be rvdw_switch and rvdw

[gmx-users] free energy calculation problem

Hi, I wanna perform free energy calculation by changing parameters of amino acid residue. Since my case is rathe complicated first I tried to perform a very simplified task - to change only charges of atoms. So I peeked out one residue, keeped all its atom types and masses and changed charges of

[gmx-users] Re: Re: crystallographic water to tip4p model

Hi, I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set -water tip4p it protonates oxygens to spc water model instead. Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? What's your GROMACS

[gmx-users] crystallographic water to tip4p model

Hi, I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set -water tip4p it protonates oxygens to spc water model instead. Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? Btw what happen if I'll

[gmx-users] distance restrainrts problem

Hi, I'm trying to apply some distance restraints to several H-bonds in my systems (all in protein) . Due to manual I added following lines [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 3880 482910 1 0.0 0.22 0.4 1.0 3880 769210 1