Re: [gmx-users] Output velocities and forces for each step?

Is there a way to split the coordinates, velocities, and forces into separate .trr files? -- Mohd Farid Ismail26.01.2018, 15:00, "Mohd Farid Ismail" <mohd.farid.ism...@yandex.com>:That does it. Thank you for your quick reply. -- Mohd Farid Ismail26.01.2018, 13:19,

Re: [gmx-users] Output velocities and forces for each step?

That does it. Thank you for your quick reply. -- Mohd Farid Ismail26.01.2018, 13:19, "Shrinath Kumar" <shrinath.ku...@ucdconnect.ie>:1. No, they are written at whatever frequency you specify in your mdp file.Look at the nstxout, nstvout and nstfout options. You can cho

[gmx-users] Output velocities and forces for each step?

is written to the .trr file?2) What switch to the mdrun do I use to have the forces for each step are written to the .trr file?3) How can one extract these velocities and forces into separate files? I've googled a little bit but couldn't find any definitive information. -- Mohd Farid Ismail

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

/10.1021/jp3002383 --Mohd Farid Ismail28.05.2015, 05:13, "Ebert Maximilian" m.eb...@umontreal.ca:I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calcul

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

What he meant was to specify full path of your cmake, i.e. /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY. (and so on); instead of just typing cmake .. -DGMX_FFT_LIBRARY This is really a linux issue instead of gromacs.  08.11.2014, 06:00, "Agnivo Gosai"

Re: [gmx-users] Problems installing Gromacs 5.0.1

What works for me was to delete everything in the build directory before re-running cmake. Give it a try and see if that helps. --Farid 30.09.2014, 22:16, Claudia Fernandes cs.fernandes0...@gmail.com: Hello everyone! I tried to install Gromacs 5.0.1. After this command: cmake ..

Re: [gmx-users] I: How to rolled up a polymer chain

. -- Mohd Farid Ismail mohd.farid.ism...@yandex.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

Re: [gmx-users] About .rtp File

at 5:45 AM, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote:  Hi, how would one use the .rtp file with pdb2gmx?  Is pdb2gmx supposed to  just find the .rtp file in the local directory?  I wanted to create an entry for a new residue using oplsaa.  However,  (assuming I build the .rtp

Re: [gmx-users] About .rtp File

, pdb2gmx just creates a position restraint file for heavy atoms automatically by default. When in doubt, check the manuals. *Joao Martins* joaomartins...@gmail.com On Tue, Sep 16, 2014 at 10:09 AM, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote:  Thank you Joao Martins.  I figured

[gmx-users] About .rtp File

' with the error Residue 'R21' not found in residue topology file. The file R21.rtp is in the local directory. -- Mohd Farid Ismail mohd.farid.ism...@yandex.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting