Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

I see. Now I understand what "pull-start" option means. Changing that option made it work! Thank you Justin. On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul wrote: > > > On 8/7/16 1:21 PM, Dan Gil wrote: > >> In Gromacs/4.6, I used init to define the distance from the solvent COM

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

On 8/7/16 1:21 PM, Dan Gil wrote: In Gromacs/4.6, I used init to define the distance from the solvent COM that the solute should be pulled to. Has it changed for Gromacs/5.1? Nothing has changed except (1) syntax and (2) the ability to now apply multiple restraints simultaneously.

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

In Gromacs/4.6, I used init to define the distance from the solvent COM that the solute should be pulled to. Has it changed for Gromacs/5.1? What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from the solvent COM? Here is the section I think you are talking about also: Pull

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

On 8/7/16 1:13 PM, Dan Gil wrote: Hi, I've made the change you suggested. The output file pullx.xvg has changed from something like: @ s0 legend "1" @ s1 legend "1 dZ" 0. 3.01072 3.01072 0.2000 2.98101 2.98101 0.4000 2.94186 2.94186 0.6000 2.95316 2.95316 to this: @ s0 legend "1" @ s1

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Hi, I've made the change you suggested. The output file pullx.xvg has changed from something like: @ s0 legend "1" @ s1 legend "1 dZ" 0. 3.01072 3.01072 0.2000 2.98101 2.98101 0.4000 2.94186 2.94186 0.6000 2.95316 2.95316 to this: @ s0 legend "1" @ s1 legend "1 dZ" 0. 3.01072 -3.01072

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

On 8/7/16 11:35 AM, Dan Gil wrote: Hi, The pullx.xvg file is returning the coordinates of the solvent, and not the solute (a_Cooh) as I want. The solute is being pulled in a coordinate other than Z, although I specify: pull-coord1-dim =N N Y What is going on here? Swap pull-coord1-groups

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Hi, The pullx.xvg file is returning the coordinates of the solvent, and not the solute (a_Cooh) as I want. The solute is being pulled in a coordinate other than Z, although I specify: pull-coord1-dim =N N Y What is going on here? On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <

Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Hi All, I'm having a similar problem and wouldn't mind some advice either. I am getting LINCS warnings on one cluster that I run my sampling on, but the pull-code works fine on other clusters we have access to, which is making me doubt the entire process. Best regards, Billy On 7 August 2016

[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Hi, I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp file that I am confused with. I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent. This is a slab geometry, with the plane normal to the z-axis direction. My output (pullx.xvg) should contain the