[gmx-users] The sign of deuterium order parameter calculated by g_order

Dear All, I am studying the effects of cholesterols in POPC lipid bilayer. The Gromacs is the version 4.6.5 in my simulations. By using the g_order, I could output the deuterium order parameter of POPC lipids for a long-term equilibration. "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

Dear Alex, Many thanks for your replies and helping. I totally agree with your comments about infinite molecules and periodic boundary condition. Here in our simulations, the hBN sheet covers the box dimensions (6nm*6nm) without free edges. By using PBC and "periodic-molecules = yes", we could

[gmx-users] (no subject)

Dear Alex, Many thanks for your replies and helping. I totally agree with your comments about infinite molecules and periodic boundary condition. Here in our simulations, the hBN sheet covers the box dimensions (6nm*6nm) without free edges. By using PBC and "periodic-molecules = yes", we could

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

Dear Justin, Many thanks for your reply and explanation. Now I understand the difference between "couple-intramol = no" and "couple-intramol = yes" and their consequences. According to the manual, it is recommended to use "couple-intramol = yes" for relatively large molecules. Why is that? I

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

Hi Alex, Thank you for your reply. Here below is my response to your comments. hBN is hardly a common subject of simulation for Gromacs folks, but let's see... 1. When you run the simulation in vacuum, do you get the same error? Does a 300K vacuum simulation

[gmx-users] Periodic Molecule's Free Energy Calculation Error

Hello Gromacs Community, I am trying to calculate the solvation free energy of a hBN sheet following Justin Lemkul and Alchemistry's tutorials. Since the hBN sheet is infinitely large, I turned the periodic molecules flag on. This runs all fine on one core, but when I try to run NVT in parallel

Re: [gmx-users] The Rationality of Position Restrain in Umbrella Sampling

9:54 AM, Jason Zhu wrote: > Dear All, > > I am modeling the free binding energy between two molecules following the > Gromacs Tutorial 3: Umbrella Sampling ( > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html > ). > > In th

[gmx-users] The Rationality of Position Restrain in Umbrella Sampling

Dear All, I am modeling the free binding energy between two molecules following the Gromacs Tutorial 3: Umbrella Sampling ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html ). In this tutorial, the Chain_B of proteins is fixed as an immobile reference by

Re: [gmx-users] Non-overlapping region appears in histograms when using SMD+Umbrella Sampling for strong binding complex

loading rate. Best, Wenpeng Zhu On 4/20/17 2:30 PM, Jason Zhu wrote: > Dear All, > > I am modeling the binding free energy between a molecule of sodium cholate > and a 2D nanosheet by using steered MD and umbrella sampling as guided by > Gromacs Tutorial 3 ( > http://www.bevanlab.bio

[gmx-users] Non-overlapping region appears in histograms when using SMD+Umbrella Sampling for strong binding complex

Dear All, I am modeling the binding free energy between a molecule of sodium cholate and a 2D nanosheet by using steered MD and umbrella sampling as guided by Gromacs Tutorial 3 ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html ). The small molecule has