[gmx-users] problem in NPT equilibration step

Dear Gromacs user, I am trying to simulate a protein (nmr structure).I have successfully done energy minimisation step.Also I have equilibrated the system a 298 k (which is achieved from 100 ps run) .Now,I am trying to equilibrate the system at 1 bar pressure.After a run of 100 ps ,I am getting

Re: [gmx-users] problem in NPT equilibration step

Hi, Parrinello-Rahman coupling usually allows wide fluctuations in the pressure. I would suggest to take Berendsen algorithm for equilibrating your system, and then extend the simulation with PR if you need to. Bests, baptiste 2013/10/14 Preeti Choudhary preetichoudhary18111...@gmail.com

Re: [gmx-users] problem in NPT equilibration step

The barostat tries to equilibrate the system at the desired pressure, there will be fluctuations and these fluctuations are little higher for Parrinello-rahman if started far away from equilibrium value. I would suggest to start from berendsen and then extend it to P-R. Also, you should run little

Re: [gmx-users] problem in NPT equilibration step

http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and http://www.gromacs.org/Documentation/Terminology/Pressure are useful here. Mark On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary srinathchowd...@gmail.comwrote: The barostat tries to equilibrate the system at the desired

[gmx-users] problem regarding npt equilibration

HI all.. I am doing npt of protein-ligand complex. Now in that error is comingPressure scaling more than 1%. How can I overcome this problem? -- [image: images[12]] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi image004.jpg-- gmx-users mailing list

Re: [gmx-users] problem regarding npt equilibration

On 16/05/2011 4:26 PM, rashi parihar wrote: HI all.. I am doing npt of protein-ligand complex. Now in that error is comingPressure scaling more than 1%. How can I overcome this problem? IIRC that's a warning, not an error. You simulation system was far enough from its equilibrium size that

[gmx-users] Problem with NPT equilibration

Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax 1000 in 1785 steps Potential Energy =

Re: [gmx-users] Problem with NPT equilibration

Bing Bing wrote: Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax 1000 in 1785 steps Potential