Re: [gmx-users] k-space settings in GROMACS

, etc.) when PME is used instead of P3M? (I have tried with some simple systems and got similar results when PME is used instead of P3M-AD) Thank you very much for your help. I really appreciate it. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] k-space settings in GROMACS

' defines the relative strength of the Ewald-shifted direct potential. Also, would there be much difference (e.g. in the energy of the molecules, in the output pressure, etc.) when PME and P3M are used? Thank you, Anh Vo

[gmx-users] k-space settings in GROMACS

in GROMACS (e.g. which command should I use ?). Also, would it make a significant difference (e.g. in the energy of the molecules, in the output pressure, etc.) if I use PME instead of PPPM in GROMACS ? Thank you very much for your help. Best, Anh Vo -- Gromacs Users mailing list * Please search

[gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules

really appreciate it. Best, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] Pressure outputs from gmx energy

for your help. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] Error when running pbs files using GROMACS on hpc cluster

s relevant to using mpirun. I don't understand what the errors mean, or how should I fix them? Please help me with this problem. Thank you very much for sharing your time. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file

e output .edr file, there are PRESS-XX, PRESS-YY and PRESS-ZZ options. > What do they represent? Are they principal pressures (stresses) averaged for > all atoms during the simulation? > What is the difference between those options and PRESSURE option? > > Thank you very much.

[gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file

) averaged for all atoms during the simulation? What is the difference between those options and PRESSURE option? Thank you very much. Best, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Stress-Strain curve plot

pened. Running with fewer ranks might avoid this issue". Is the Domain Decomposition automatically set in GROMACS for running simulation and how to avoid this problem? Thank you very much. Anh Vo >> >> -Original Message- >> >> Message: 6 >> >> Da

Re: [gmx-users] Parrinello-Rahman vs. Nose-Hoover

t know why that is the most practical choice? And *why is Nose-Hoover not used for pressure coupling in GROMACS as it is used in LAMMPS?* Thank you a lot. Best, Anh Vo > > -Original Message- > > > Message: 3 > > Date: Wed, 29 May 2019 00:51:41 +0200 > > From: Mark Ab

Re: [gmx-users] Stress-Strain curve plot

ction around cell 0 0 3. This should not have happened. Running with fewer ranks might avoid this issue" Thank you, Anh Vo > > -Original Message- > > Message: 6 > > Date: Wed, 29 May 2019 01:00:55 +0200 > > From: Mark Abraham > > > > Hi, >

Re: [gmx-users] Timestep in GROMACS simulation

Hi, I'm still not clear what "sampling" means. Does it mean collecting data from the simulation? Thank you very much for your answer. Best, Anh Vo -Original Message- > > > Message: 4 > > Date: Tue, 28 May 2019 20:43:32 -0400 > > From: Kevin Boyd &

[gmx-users] Explaination of some terminology

is ergodic, the ensemble average becomes equal to the time average”. What does it means if a system is ergodic? Why does ensemble sampling becomes similar to time sampling if a system is ergodic? Thank you very much. Best, Anh Vo -- Gromacs Users mailing list * Please search

[gmx-users] Timestep in GROMACS simulation

Why does the larger time step allow better sampling? Thank you a lot. Best, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Parrinello-Rahman vs. Nose-Hoover

r not used for pressure coupling in GROMACS? Thank you very much. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Stress-Strain curve plot

. This should not have happened. Running with fewer ranks might avoid this issue”. What does this error mean? What is domain decomposition? Is the Domain Decomposition automatically set in GROMACS for running simulation? Thank you very much for sharing your time. Sincerely, Anh Vo -- Gromacs Users

[gmx-users] von Mises stress-strain curve

you very much for sharing your time. Sincerely, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe request

Re: [gmx-users] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

bined with the Nose-Hoover thermostat as the most practical choice", and I see that Nose-Hoover algorithm is only available for temperature coupling, not pressure coupling. Why is Nose-Hoover not used for pressure coupling in GROMACS? Thank you very much. Best regards, Anh Vo -- Gromacs Users ma

[gmx-users] Differences between Parrinello-Rahman, Nose-Hoover and MTTK - between LINCS and SHAKE

does "refcoord_scaling" do in pressure coupling? Thank you very much for sharing your time. Best regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.g

[gmx-users] How to calculate Stress Strain curve in GROMACS

to solve this problem? Thank you very much. Regards, Anh Vo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests