Re: [gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

2012-09-20 Thread Mark Abraham
On 20/09/2012 5:08 PM, Ladasky wrote: Mark Abraham wrote This all sounds much like an issue with the topology or starting configuration. And it is for that reason that, during my debugging process, I switched back from the chimeric protein structures that I was building myself to a standard PDB

Re: [gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

2012-09-20 Thread Mark Abraham
On 20/09/2012 4:34 PM, Ladasky wrote: Justin Lemkul wrote So the initial equilibration was NPT? Yes. Justin Lemkul wrote Did you ever try simply running NVT with either Berendsen or V-rescale before applying any type of pressure coupling? No, I haven't, and I don't remember seeing that desc

[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

2012-09-20 Thread Ladasky
Mark Abraham wrote > This all sounds much like an issue with the topology or starting > configuration. And it is for that reason that, during my debugging process, I switched back from the chimeric protein structures that I was building myself to a standard PDB structure for which I had previous

[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

2012-09-19 Thread Ladasky
Justin Lemkul wrote > So the initial equilibration was NPT? Yes. Justin Lemkul wrote > Did you ever try simply running NVT with > either Berendsen or V-rescale before applying any type of pressure > coupling? No, I haven't, and I don't remember seeing that described in any work flow. Justin