Re: [gmx-users] Can't observe ion separation under the influence of electric field

utational Modeling of Biological Processes, > Institute of Molecular Biology, NAS, Armenia, Yerevan > Tel: +374 93 323990 > h_sahak...@mb.sci.am > sahakya...@gmail.com > > February 13, 2020 2:07 AM, "Live King" wrote: > > > Dear all, > > > > I am ru

[gmx-users] Can't observe ion separation under the influence of electric field

Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not

[gmx-users] Electric field settings in GROMACS

Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not

[gmx-users] Free energy calculations with membrane

Hi everyone, I am trying to do Justin's thermodynamic integration tutorial with a lipid bilayer. I believe the energy I will get from this exercise is the energy required to take alanine from membrane to vacuum. I have placed my alanine at the center of bilayer. Does this energy output contain

[gmx-users] Problem with gmx genion

Dear all, I am using martini polarisble FF and I have generated mixed lipid bilayer containing (DOPC-DOPS). I am trying to neutralise the system by adding NA using this commnad *gmx genion -s ions.tpr -o ionized.gro -p topol.top -pname NA -nname CL -neutral* I replace PW (water molecules) with

[gmx-users] Issue in Steep descent minimization (Free energy calculation)

Hi everyone, I know this issue has been addressed several times but I couldn't find the solution for my problem. So, I had to ask here. I am trying to calculate free energy using martini forcefield. My system has water, DPPC bilayer and membrane protein embedded in it. After steepest descent

[gmx-users] Free Energy calculations with GROMACS 5.0.5 on cluster

Hi everyone, I am running free energy calculations on my cluster using GROMACS 5.0.5. I have 21 windows so, I run my simulations parallely. I am fairly new to GROMACS 5.0.5 and had used version 4.5.5 before. In that case I used "-np 2" or "-np 1 " option of mdrun to run parallel simulations.

Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis

of Live King vikasdubey1...@gmail.com Sent: Wednesday, August 26, 2015 5:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Pull parameters to Restrain motion along the Z Axis Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein

[gmx-users] Pull parameters to Restrain motion along the Z Axis

Hi, I use Gromacs 4.5.5. I have these pull parameters which I use to restrain my Protein motion along the Z axis.I want to make sure these parameters are fine or not since , I am not getting expected results. Also, please suggest any other parameters I can add. ;Pull to restrain Z position pull

[gmx-users] Gromacs Path

Hi Everyone, I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs, then what is path of my Gromacs directory ? I don't seem to find it anywhere . Thanks, vikas -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Free Energy Calculations

Hi Everyone, I use ancient version of Gromacs 4.5.5 for free energy calculations. I have two different questions. 1) When I run g_bar for results, I get this lambda 0.000 - 0.050, DG -2.16 +/- 0.00 lambda 0.050 - 0.100, DG -2.16 +/- 0.01 lambda 0.100 - 0.150, DG -2.09 +/- 0.01