Re: [gmx-users] Re: Steepest Descents in vacuo

On 6/14/13 7:22 AM, maggin wrote: Hi, Justin, If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest Descents in vacuo first ? I have no idea. There are many ways you can probably dream up to proceed with any system. For normal proteins in water, I never waste time with

[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin, If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest Descents in vacuo first ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009153.html Sent from the GROMACS Users Forum mai

Re: [gmx-users] Re: Steepest Descents in vacuo

Constraints make the job of the minimizer more difficult. If the starting configuration is bad enough that the EM step might be really useful, give the potential energy surface a free run without constraints. And then in such cases do a preliminary NVT with dt=0.0005 and no constraints to get thing

[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin, Thank you very much for your help! Another question is when we do steep minimization, if it will be better first do steep with constraint, then do steep without constraint? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-D