Re: [gmx-users] Steered MD in gromacs

2013-09-03 Thread Gianluca Interlandi
On 9/3/13 3:10 PM, Gianluca Interlandi wrote: Also, why in vacuo? At least turn on an implicit solvent model. I can think of reasons to study molecular interactions in vacuo via pulling. I'm sure there are. G Why is solvent (explicit or implicit) an absolute requirement? -Justin On Tue

Re: [gmx-users] Steered MD in gromacs

2013-09-03 Thread Justin Lemkul
On 9/3/13 3:10 PM, Gianluca Interlandi wrote: Also, why in vacuo? At least turn on an implicit solvent model. I can think of reasons to study molecular interactions in vacuo via pulling. Why is solvent (explicit or implicit) an absolute requirement? -Justin On Tue, 3 Sep 2013, Justin Le

Re: [gmx-users] Steered MD in gromacs

2013-09-03 Thread Gianluca Interlandi
Also, why in vacuo? At least turn on an implicit solvent model. Gianluca On Tue, 3 Sep 2013, Justin Lemkul wrote: On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tu

Re: [gmx-users] Steered MD in gromacs

2013-09-03 Thread Justin Lemkul
On 9/3/13 11:22 AM, hanna pdb wrote: Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tuto

[gmx-users] Steered MD in gromacs

2013-09-03 Thread hanna pdb
Dear all, I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples that were done in gromacs? In my case the tutorial " Pull Code and Umbrella Sampling"