Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Hi Simone, The temperature coupling might be a cause for an error like that to occur. Try to understand that coupling ions separately may cause large fluctuations in there velocities and hence cause sudden large displacements that may put an ion on top of a solvent molecule that can't be settled a

Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Simone Cirri wrote: Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately. Surely

Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups > Tcoupl = berendsen > > tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ > > ref_t = 300 300 300 > > Never couple solvent and ions separately. Surely grompp warned you that you > shou

Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Simone Cirri wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately.

[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

Hi everyone, in the last weeks I've been trying to run a simulation with Gromacs 4.0.5 and the force field ffamber99. The protein is albumine (BSA, bovine serum albumine), so it's a very big one (570+ residues). The solvent is tip3p. After an energy minimization run and a position restraint run, I