Re: [gmx-users] Gentle heating with implicit solvent

I wonder whether increasing the surface tension parameter sa-surface-tension might solve the problem with the protein unfolding. Thanks, Gianluca On Mon, 4 Nov 2013, Gianluca Interlandi wrote: Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating

Re: [gmx-users] Gentle heating with implicit solvent

Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating (please note that -DPOSRES is commented out) and the time step is 1 fs: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = ;defi

Re: [gmx-users] Gentle heating with implicit solvent

On 11/4/13 2:25 PM, Gianluca Interlandi wrote: Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated

Re: [gmx-users] Gentle heating with implicit solvent

Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated annealing for the heating with 1 fs time step.

Re: [gmx-users] Gentle heating with implicit solvent

It can be. Lack of explicit degrees of freedom of solvent can make achieving equipartition tricky. With CHARMM27 and virtual sites in implicit solvent, I have sometimes found it necessary to use a sub-femtosecond time step at the start of equilibration, even where there were no atomic clashes. Mayb