[gmx-users] Dielectric constant calculation

Greetings! I was trying to calculate the dielectric constant of my system (1,4-dioxane and water), and I have encountered some problems. I gave the command to calculate dipole moment and related data, since it is a prerequisite for the dielectric calculation: gmx dipoles -f sol1ns2.trr -s sol1n

[gmx-users] GROMACS mdrun

Hi, While running an MD job for 10 ns, the system restarts in the final step of MD (mdrun -v -deffnm md) This happens continuously, and the data are not generated. What system settings should I make, to make it run continuously until finishing all the steps? Thank you. -- Shilpa J Department of

Re: [gmx-users] trr file

Hi Rita, If none of this works, you can try a to do a rerun (run mdrun with the flag -rerun). You can provide a new mdp where you can tell gromacs to write an xtc with the frequency output that you want (using a lower frequency will generate a smaller xtc file) Good work! On Sat, Oct 15, 2016 at

Re: [gmx-users] GROMACS mdrun

Hi, What are all the GROMACS commands you have been using for this simulation? Why do you think it is not finishing all the steps? Mark On Sat, 15 Oct 2016 10:55 Shilpa Janarthanan wrote: > Hi, > While running an MD job for 10 ns, the system restarts in the final step of > MD (mdrun -v -deffnm

Re: [gmx-users] Dielectric constant calculation

On 15/10/16 10:02, Thejus Kartha wrote: Greetings! I was trying to calculate the dielectric constant of my system (1,4-dioxane and water), and I have encountered some problems. I gave the command to calculate dipole moment and related data, since it is a prerequisite for the dielectric calcula

Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html You will also need to set the following variable at install time: -DGMX_QMMM_MOPAC=ON -- Clinton King Graduate Student Chemistry Department Brigham Young University > >1. QMMM install on GMX5.1 (Xianchi Dong) > > > Messag

[gmx-users] parameters for PbSe (quantum dot)

Dear all, I want to simulate the quantum dot PbSe (QD) by gromacs and amber 99sb FF. but, as you know, gromacs doesn't know this QD and its MD parameters is not exist. how can I find the Lennard jones parameters and partial charges for this QD? best regards, -- ***

Re: [gmx-users] trr file

Hi Rita, How long did your simulation run? If it happens to be very long and you do not want to run the simulation again, perhaps you can try analyzing it in pieces. Use trjconv with -b and -e options to extract small pieces of the .trr file at a time. Analyze the small pieces, delete the .xtc fi

Re: [gmx-users] Dielectric constant calculation

Thank you. I am using 5.1.2 version, maybe that's why. Let me check this out. On Saturday, 15 October 2016 9:20 PM, David van der Spoel wrote: On 15/10/16 10:02, Thejus Kartha wrote: > Greetings! > I was trying to calculate the dielectric constant of my system (1,4-dioxane > and water