[gmx-users] NPT Simulation average pressure lower than Reference set pressure

Dear Users I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS 4.5.7 single precision. My earlier work flow 1) Topology preparation 2) Box , Solvation and Ions 3) Energy minimization - Steepest descent 4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K aver

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

I would recommend 200,000 time steps to try to get accurate pressure readings. Pressure, I believe, is computed from the virial and can fluctuate a lot. Also, adjust nstcalcenergy and nstenergy to a small number, I use 10 to get more accurate pressure readings. You should have noticed the error

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

Hi, It's not about adding points. The statistics are over all time steps already. However, it should be noted that at t=0 the pressure was not controlled yet. So these statistics include the convergence and are therefore unlikely to reproduce the reference pressure. In addition, there is the quest

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

Sampling over 100 ps is incredibly meaningful... Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Thu, Oct 30, 2014 at 6:49 AM, Agnivo Gosai wrote: > Dear Users > > I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS > 4.5.7 single precision. > > My earlier work flow > 1) T

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

ation average pressure lower than Reference set pressure Sampling over 100 ps is incredibly meaningful... Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Thu, Oct 30, 2014 at 6:49 AM, Agnivo Gosai wrote: > Dear Users > > I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in G

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

Dear Users Dr. Micholas : Do you suggest that I do a longer run ? I am doing another NPT carrying on from the previous NPT with a Parrinello-Rahman barostat. I am attaching the NPT pressure and density plots , if anyone wants to have a look at them. Dr. Vitaly : I was thinking that my equilibrati

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

Hi Agnivo, No, I was not hinting at a running average. The average of a parameter over a certain time is a single observation, which has a certain distribution, with the mean equal to the population (infinite time) mean, and some standard deviation. I have posted before about this in relation to p

Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

Oh, I mean a single observation from a certain distribution... T. On Fri, Oct 31, 2014 at 9:31 PM, Tsjerk Wassenaar wrote: > Hi Agnivo, > > No, I was not hinting at a running average. The average of a parameter > over a certain time is a single observation, which has a certain > distribution, w