[gmx-users] Re: Details of umbrella sampling simulation

Hi, Please see the following links: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/ http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html I think you will understand the concept of the pulling force once you go through either of the links. It's basical

[gmx-users] Re: Free Energy Calculations in Gromacs

Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did indeed solve a lot of my problems. Thanks again. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html Sent from the GROMACS Users Forum mailing list

[gmx-users] Re: Membrane Equilibration

Is there a reason you would like to keep it at 105K? Just curious which forcefield are you using? Also, for proper surface tension, there is an option called pcoupltype = surface-tension. I think you should check that out. -- View this message in context: http://gromacs.5086.x6.nabble.co

[gmx-users] Re: Membrane Equilibration

Exactly so. I think Gromacs issues a warning when you try to initialize velocities with Parrinello-Rahman barostat. But if you performed your equilibration at 105K using Berendsen barostat, I think it should be okay and you should put gen-vel = no. -- View this message in context: http://groma

[gmx-users] Re: restraints on water oxygen atoms

Hi, As Justin had already suggested, restraints will lead to nasty atomic clashes. Looking at the gro file you have provided, it seems that the system is very poorly equilibrated. I had a similar issue. If the forcefield you are using is accurate enough, follow the steps as follows: 1. Take th

[gmx-users] Re: Free Energy Calculations in Gromacs

Hi, I have been trying to perform the simulations using the amber forcefield, in which the [ pairtypes ] directive is not defined explicitly in the ffnonbonded.itp file, but rather the 1-4 interactions are generated as per the defaults section in the forcefield.itp file. I was wondering what happe