[gmx-users] error while running mdrun

Dear all, While running mdrun using following mdpparameters: title= Model MD ; Run parameters integrator= md nsteps= 500 dt= 0.002 ; Output control nstxout= 500 nstvout= 500 nstxtcout= 500 nstenergy= 500 nstlog= 500 nstcomm

Re: [gmx-users] problem in running md simulation

with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee < ananyachat

[gmx-users] problem in running md simulation

Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as foll

Re: [gmx-users] how to restart a stopped simulation

, Kavyashree M wrote: Hi Ananya, You can refer this. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee < ananyachatter...@iiserkol.ac.in> wrote: Hi all, my simulation has stopped due to power failure, can

[gmx-users] how to restart a stopped simulation

Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

[gmx-users] how to check the intermediate coordinated even when the simulation is running

I am very new to this MD simulation, by reading the tutorials in the website I have run an simulation and it is running from last 5 day and I am not getting whether it is running properly or not. Could any one kindly tell me how to see whether the simulation is running or not and also how can