Re: [gmx-users] -rerun with energygrps

This is 2018, I will compare later. The issue is mostly sort of solved, as I just moved all of electrostatics to 'cut-off' with a large radius for the rerun. I first thought it was because the system was not neutral (ion + water without the counterion, so it refused to report the PME part),

Re: [gmx-users] -rerun with energygrps

Hi, What version is this? What does gmx compare report amwhen comparing the two tpr files? Mark On Mon, Apr 9, 2018, 22:54 Alex wrote: > Hi all, > > Something funny is happening. I have a very simple system: an ion in bulk > TIP4P water running under OPLS-AA. mdp excerpt

[gmx-users] -rerun with energygrps

Hi all, Something funny is happening. I have a very simple system: an ion in bulk TIP4P water running under OPLS-AA. mdp excerpt below: nstlist = 20 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1.0 coulombtype = pme

Re: [gmx-users] problem in running job.sh for free energy calculations.

Thanks sir Mark and Justin. I ll try to figure it out with the administer. But in case the problem is not resolved, is it okay if I run the commands directly through terminal? Will it effect the results? I know it ll be a tedious job. Regards Neelam Wafa On Mon, 9 Apr 2018 10:03 pm Justin

Re: [gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

Hi, It's on our to-do list, but there are no concrete plans (and definitely no working code). Sorry! Mark On Thu, Apr 5, 2018, 22:57 Christopher Neale wrote: > Dear Kevin: > > > Perhaps I misstated my goals. I am not saying that GPUs don't ever help. I > am

Re: [gmx-users] problem in running job.sh for free energy calculations.

On 4/9/18 12:56 PM, neelam wafa wrote: Thanks Sir for your quick response. These are the errors I am getting. Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist or is not accessible.

Re: [gmx-users] using constant velocities during simulation

Hi, I don't follow. Constant velocities can't be consistent with a dynamical simulation with forces between particles. Mark On Fri, Apr 6, 2018, 19:30 Qasim Pars wrote: > Dear users, > > I would like to use the constant velocities for all the atoms of both > protein and

Re: [gmx-users] problem in running job.sh for free energy calculations.

Hi This is how I modified the job.sh script #!/bin/bash # Set some environment variables FREE_ENERGY=/home/Downloads/Free_Energy echo "Free energy home directory set to $FREE_ENERGY" MDP=$FREE_ENERGY/MDP echo ".mdp files are stored in $MDP" LAMBDA=0 # A new directory will be created for each

Re: [gmx-users] gmx select and gmx trjconv or gmx density

Hi, Unfortunately not all tools support dynamic selection groups yet, so the only useful way to use that index file is by matching it with the correct single frame from the trajectory, which you might get from e.g. gmx trjconv split Mark On Fri, Apr 6, 2018, 21:37 Dan Gil

Re: [gmx-users] problem in running job.sh for free energy calculations.

Thanks Sir for your quick response. These are the errors I am getting. Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist or is not accessible. In command-line option -c File

Re: [gmx-users] High pressure in coarse-grained parametrization

Hi, Instantaneous pressure is meaningless. You should get roughly the same behavior with me integrator. Mark On Sat, Apr 7, 2018, 04:13 Alex wrote: > Dear all, > > Here is a part of the *.mdp file I am using in coarse-grained > parametrization (Iterative Boltzmann

Re: [gmx-users] Carbon-Alpha RMSD Plots

Hi, The header in your xvg file confirms how you ran the analysis, and your simulation .log file confirms what you actually did. As does gmx check on your trajectory file. Mark On Mon, Apr 9, 2018, 17:53 jt555 wrote: > Hello there, > > I am writing to seek clarification

Re: [gmx-users] problem in running job.sh for free energy calculations.

Hi, Probably your initial working directory is not what you expect it to be. That's often supposed to be set in your job script. Check out the documentation for your cluster or submission system, and then ask the admins. Mark On Mon, Apr 9, 2018, 17:25 neelam wafa wrote:

[gmx-users] Carbon-Alpha RMSD Plots

Hello there, I am writing to seek clarification regarding the following: I use GROMACS version 5.1.2 and Grace (xmgrace) version 5.1.25 I ran a molecular dynamics simulation for 1 microsecond (~ 1055 ns). I used xmgrace to plot a carbon-alpha RMSD plot and I noticed that the x-axis [Time

Re: [gmx-users] problem in running job.sh for free energy calculations.

On 4/9/18 11:25 AM, neelam wafa wrote: Dear sir Justin I am doing your tutorial of free energy calculations for methane in water. I have created the .mdp and .sh files using the perl script you provided. I have also made the FREE_ENERGY and MDP directories as in the job. sh script. gro file

[gmx-users] problem in running job.sh for free energy calculations.

Dear sir Justin I am doing your tutorial of free energy calculations for methane in water. I have created the .mdp and .sh files using the perl script you provided. I have also made the FREE_ENERGY and MDP directories as in the job. sh script. gro file and topology files are also in the

[gmx-users] golp-CHARMM

Hi everyoneI want to simulate carboxylic acid self-assembled monolayer on a goldsurface with Golp-charmm parameters for Au(111) in Aqueous environment.[ref: J. Chem. Theory Comput. 2013, 9, 1616−1630].GolP-CHARMM parameters forthe Au(111) surface are presented in Table 2:  Surfacea            

Re: [gmx-users] Problem with CUDA

Thanks. That was already set by cuda module. Didn't help me. Chris -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Szilárd Páll Sent: Saturday, April 07, 2018 11:28 AM To: Discussion

Re: [gmx-users] viscosity calculation using g_energy

Den 2018-04-08 kl. 17:31, skrev Ali Ahmed: Hello David, Thank you for your reply, After 5 ns of equilibrium, I run the simulation for 10 ns of heptane, but in the results of Einstein viscosity, I got only 5 ns. There are two files evisco.xvg and viscosity .xvg. In the first one, there are