Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

how long were those simulations? Were there enough time for the new ensemble to equilibrate, if you changed ensemble from NVE to NVT? On Sun, Oct 19, 2014 at 11:34 AM, Wade wrote: > Dear Mark and Lu, > Thank you very much for your responses. > Based on your suggestions, I performed some tests:

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Dear Mark and Lu, Thank you very much for your responses. Based on your suggestions, I performed some tests: 1) I considered the influence of the time-step (with LINCS constraint), thermostat, and simulation precision in NVT simulation (tip4p water box, 300K, after 2ns NVE simulation). Below

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

From Bussi paper: "If we use this analysis and go to the limit of an infinitesimal time step, we find [Equation 15] where the last two terms come from the integration of Eq. 7 along the trajectory. Note that a similar integration along the path is present in H_{Nosé}. However, in our scheme a stoch

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

The bussi paper is at [ marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf ]. I seem to vaguely remember someone wrote if tilde H drop linearly, it means the energy is conserved. But I'm not sure now. On

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Figure 2 of the Bussi paper has a diagram with constant tilde H for NVT simulation with 2fs time step, and another one with rising tilde H for NVT simulation with 40fs timestep, and say: "for tilde H in the NVT calculation. We notice that, while in the NVE calculation the system explodes at some po

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Does this old maillist post say tilde H is conserved energy? [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ] On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham wrote: > On Sat, Oct 18, 2014 at 4:32 PM, Wade wrote: > > > Dear Mark, > > Thank your very muc

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

On Sat, Oct 18, 2014 at 4:32 PM, Wade wrote: > Dear Mark, > Thank your very much for your reply. However, I still confused because > results showed that the conserved En. was time dependent (with small > fluctuation); but, the total energy in the ener file has small drift with > high fluctuat

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Does double precision cause a less drop/rise in tilde H over time, when compared to a mixed precision run under same condition ? On Sat, Oct 18, 2014 at 11:28 AM, Johnny Lu wrote: > Oh, integrating with rectangles under the curve causes error. I guess > larger time-steps can cause error in tilde

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Oh, integrating with rectangles under the curve causes error. I guess larger time-steps can cause error in tilde H by this method of integration alone. On Sat, Oct 18, 2014 at 11:25 AM, Johnny Lu wrote: > For V-rescale thermostat, the bussi paper seems to say the tilde H is the > integral of the

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

For V-rescale thermostat, the bussi paper seems to say the tilde H is the integral of the auxiliary dynamics. Not sure if this is same as the conserved energy in gromacs, which is also the integral of the auxiliary dynamics. I guess numerical error causes the system to lose/gain total energy in a

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

Dear Mark, Thank your very much for your reply. However, I still confused because results showed that the conserved En. was time dependent (with small fluctuation); but, the total energy in the ener file has small drift with high fluctuations. Further, I rechecked the code (gmx-4.5.5) ?in