[gmx-users] Errors with g_dielectric

Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked t

[gmx-users] Segmentation Fault with g_dielectric

Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked t

[gmx-users] Selecting specific atoms to find average energy of

Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules, excluding the energy between the solute-solvent molecule

Re: [gmx-users] Concerns with g_wham

code designations dictate a? Thanks, Jennifer On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub wrote: > Jennifer Casey wrote: > >> Hello, >> >> I have been using g_wham, but I have a few questions that I can't find >> answers to online. When using WHAM, one does not need

[gmx-users] Concerns with g_wham

Hello, I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? Also, when using the pull code, I am allowed

[gmx-users] Problems with umbrella sampling

Hello, I am interested in creating a PMF for Na+ and I- in the presence of THF (tetrahydrofuran). I am having a couple of issues though. First, I have followed the umbrella sampling tutorial on the gromacs website very careful, and I think I am doing everything right. I minimized the energy of

Re: [gmx-users] Problems wtih g_wham

Thank you so much! I appreciate the help, and the good news is actually great news. Jenny On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub wrote: > Jennifer Casey wrote: > >> Hello, >> >> I am trying to create a PMF for the sodium cation and iodine anion in the >>

Re: [gmx-users] Problems wtih g_wham

I will change pull = constraint to pull = umbrella and see if I still get the error. Thanks, Jenny On Fri, Feb 12, 2010 at 6:12 PM, Justin A. Lemkul wrote: > > > Jennifer Casey wrote: > >> Hello, >> >> I am trying to create a PMF for the sodium cation and iodine anion in

[gmx-users] Problems wtih g_wham

Hello, I am trying to create a PMF for the sodium cation and iodine anion in the presence of THF. I have been following the umbrella sampling tutorial on the gromacs website, and everything has been working out. I have finally created 14 different equilibriation simulations, whose starting confi

Re: [gmx-users] Restrained Molecule is Moving

, 1.621). Maybe this is normal amount of drift? Thanks again, Jenny On Tue, Feb 2, 2010 at 6:01 PM, Justin A. Lemkul wrote: > > > Jennifer Casey wrote: > >> Hello, >> >> I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) >> of my box of di

[gmx-users] Restrained Molecule is Moving

Hello, I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of 253 THF molecules. I added the following to the bottom of my .itp file: #ifdef POSRES #include "posre_Na+.itp" #endif I wrote the posre_N

[gmx-users] Questions about Pull Code

Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a trajectory of configurations along