Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

Hi, On Tue, 26 Apr 2016 06:19 Husen R wrote: > Hi all, > > I tried to run this gromacs tutorial ( > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html > ) > in order to understand how checkpoint/restart works in Gromacs-5.1.2. > >

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

Hi all, I tried to run this gromacs tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html) in order to understand how checkpoint/restart works in Gromacs-5.1.2. Based on running that tutorial I found that mdrun automatically checkpoint even

Re: [gmx-users] [gmx-developers] MD Units

Hi, I fixed the definition to be bar, and removed some other stuff I think is unnecessary at https://gerrit.gromacs.org/#/c/5826/ Mark On Mon, Apr 25, 2016 at 9:22 PM Erik Lindahl wrote: > Hi Adam, > > The stuff you get from the energy file should be bars. The first

Re: [gmx-users] how to convert CHARMM36 system into virtual site system?

On 4/24/16 2:19 PM, Albert wrote: Hello: I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just wondering how can we convert the lipids molecule to virtual site lipids? Presumably you'll have to create a .vsd file, but I've never validated such an approach with C36. The

Re: [gmx-users] Higher Density than Expected

On 4/25/16 5:09 PM, Christopher Schlicksup wrote: Hi, I am fairly new to simulation, and would like some input about whether I have set up Gromacs correcly. I am using version 5.0.4 with the CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a 35kDa protein in a

[gmx-users] Higher Density than Expected

Hi, I am fairly new to simulation, and would like some input about whether I have set up Gromacs correcly. I am using version 5.0.4 with the CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus neutralizing

Re: [gmx-users] [gmx-developers] MD Units

Hi Adam, The stuff you get from the energy file should be bars. The first chapters is more about documenting the “natural” internal units, but we should probably clarify this. Cheers, Erik > On 25 Apr 2016, at 21:17, Rigby, Adam wrote: > > Dear All > > Are the MD

Re: [gmx-users] Problem in auto source

Hi, Can you try source /usr/local/gromacs/bin/GMXRC.bash ? I had the same problem and this works for me. Best, Irem >> > On Apr 25, 2016, at 3:08 PM, Roshan Shrestha wrote: > > This is my .bashrc file and it looks like this- > >> # ~/.bashrc: executed by bash(1) for

[gmx-users] Problem in auto source

This is my .bashrc file and it looks like this- > # ~/.bashrc: executed by bash(1) for non-login shells. > # see /usr/share/doc/bash/examples/startup-files (in the package bash-doc) > # for examples > > # If not running interactively, don't do anything > case $- in > *i*) ;; > *)

Re: [gmx-users] REMD--how to determine the temperature distribution

There are many published approaches. Here is the one that I use: http://origami.phys.rpi.edu/racc/rate_of_acceptance.php Another example is here: http://folding.bmc.uu.se/remd/ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

[gmx-users] REMD--how to determine the temperature distribution

Dear all, I am going to run a REMD of a protein(explicit solvent) in NVT ensemble with gromacs, but I have trouble in determining a optimum temperature distribution.Can anybody know the ways to determine the temperature? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Potential shift

Hi, It's often nice as a user to know that the program has agreed with your intentions :-) You're using a tabulated interaction, so AFAICR mdrun just does what you say. In some cases, mdrun will generate tables to implement the user's short-ranged options, and it's important that mdrun says what

[gmx-users] Potential shift

Dear GMX users, Does anybody know why the "Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00" is written in my case.log file in spite of using LJ(6-9) in my calculations? Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Cut-off's: NS: 1 Coulomb: 1.26

[gmx-users] Fwd: how to convert CHARMM36 system into virtual site system?

Hello: I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just wondering how can we convert the lipids molecule to virtual site lipids? Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at