[gmx-users] non zero free energy values in mass transformation

Dear Gmx Users I am trying to find out free energy of transforming one neutral LI to one CL in aqueous solution. Water model is SPC/E. Gromacs version: 5.1.2 I am doing something like this Insert 1 Li olecule in water. (Li parameters were taken from Kasper P. Jensen and William L. Jorgensen

Re: [gmx-users] non zero free energy values in mass transformation

Deepak, I never did a mass perturbation myself, but I would expect some free energy change, since the translational partition function depends on the mass of the molecules. Also, having the same kinetic energy is not meaningful at all, the correct quantity you should always use in statistical

[gmx-users] Pull Code: direction-periodic with 3 dimensions

Hello, I am using a pull code to increase the end-to-end distance of a protein (included below). I am using direction-periodic and would like the distance between the COM groups to be calculated in three dimensions. However, setting pull_coord1_dim = Y Y Y appears to have no effect and the

[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Hi, I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running macOS 10.12.6. I can get it to compile fine and it can run my own simulation fine on CPU only, but I am having difficulty getting to work with the GPU (FirePro D500). Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on

Re: [gmx-users] Pull Code: direction-periodic with 3 dimensions

On 8/11/17 5:02 PM, Daniel Kozuch wrote: Hello, I am using a pull code to increase the end-to-end distance of a protein (included below). I am using direction-periodic and would like the distance between the COM groups to be calculated in three dimensions. However, setting pull_coord1_dim = Y

Re: [gmx-users] non zero free energy values in mass transformation

Thank you Andre and Dan. I'll read more about. Deepak On Fri, Aug 11, 2017 at 7:35 PM, Dan Gil wrote: > Hi Deepak, > > I am battling the same problem too. I am doing free energy calculation for > heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1. > >

Re: [gmx-users] (no subject)

Hi Iman, If I understand, you are planning on calculating the surface tension of water? To me, it seems odd that you would try to apply a surface-tension couple to your system, and then calculate the surface tension. Dan On Thu, Aug 10, 2017 at 5:42 AM, Iman Ahmadabadi

Re: [gmx-users] Non bonded interaction mapping

Hi Sameer, There is a quick and easy way to visualize hydrogen bonds. Convert your traj.trr file to .gro and open it in VMD software. You can then manipulate VMD options to show hydrogen bonds. Dan On Sun, Aug 6, 2017 at 10:57 AM, Sameer Edirisinghe wrote: > Dear all, > > I

Re: [gmx-users] non zero free energy values in mass transformation

Hi Deepak, I am battling the same problem too. I am doing free energy calculation for heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1. Like Andre said, there is expected to be a free energy change when you change the mass of a particle. But if you do the same transformation