Re: [gmx-users] Microcanonical MD with PBC

Lee-Ping Wang wrote: Hi everyone, I've been trying to get a microcanonical (energy conserving, NVE) MD run with periodic boundary conditions. I'm using the provided box of 216 water molecules and the SPC force field (flexible). When I turn PBC off, the energy RMSD is <0.01kJ/mol with a 0.1fs t

[gmx-users] Microcanonical MD with PBC

Hi everyone, I've been trying to get a microcanonical (energy conserving, NVE) MD run with periodic boundary conditions. I'm using the provided box of 216 water molecules and the SPC force field (flexible). When I turn PBC off, the energy RMSD is <0.01kJ/mol with a 0.1fs time step (energy is con

[gmx-users] Microcanonical

You should use neither, at least not for Coulomb. Only PME can be used for systems containing charges. For system containing exclusively neutral molecules, you can use a shift function, if the cut-off is longer than the range of the interaction. For water that would be roughly 1.2 nm. Be that

Re: [gmx-users] Microcanonical

A B wrote: Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11. Yes, this is exactly what I mean - an appropriate smoothing function ("shift") works fine, but simple group-based truncation does not; that this does not work has indeed been known since long before GROMACS was

[gmx-users] Microcanonical

Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11. Yes, this is exactly what I mean - an appropriate smoothing function ("shift") works fine, but simple group-based truncation does not; that this does not work has indeed been known since long before GROMACS was born. Mayb

Re: [gmx-users] Microcanonical

can you please send this paper to me? email address : [EMAIL PROTECTED] regards, karamyog.On 5/22/06, David van der Spoel <[EMAIL PROTECTED]> wrote: A B wrote:> I am curious about the reason for the heating that allegedly occurs with> cutoffs in NVE simulations ("The use of (electrostatic) cutoff

Re: [gmx-users] Microcanonical

A B wrote: I am curious about the reason for the heating that allegedly occurs with cutoffs in NVE simulations ("The use of (electrostatic) cutoffs is well known to cause heating in NVE simulations."). This should not, and does not, happen if an appropriate smoothing function is applied. Does t

[gmx-users] Microcanonical

I am curious about the reason for the heating that allegedly occurs with cutoffs in NVE simulations ("The use of (electrostatic) cutoffs is well known to cause heating in NVE simulations."). This should not, and does not, happen if an appropriate smoothing function is applied. Does this heating

Re: [gmx-users] microcanonical

karamyog singh wrote: I guess since after the first run, the forces between atoms is not zero(only negligible), when i do the 2nd run, the atoms start moving under the action of these forces and since there is no temperature scaling or pressure scaling, we can or might see an increase in KE as

Re: [gmx-users] microcanonical

I want a constant energy simulation at 0.01 K . Is it possible. I cannot keep increasing my cut off because for that i have to increase my box size. I have tried so many times but the temperature increases and neither is the energy constant. :( - karamyog. :(On 5/19/06, karamyog singh <[EMAIL PROT

Re: [gmx-users] microcanonical

I guess since after the first run, the forces between atoms is not zero(only negligible), when i do the 2nd run, the atoms start moving under the action of these forces and since there is no temperature scaling or pressure scaling, we can or might see an increase in KE as in my case. So an increase

Re: [gmx-users] microcanonical

karamyog singh wrote: Well, I am back. Remember my first and second mdruns. In my second, after stablizing my initial configuration in the 1st md run, I used cut off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite large a distance compared to 0.309. In the second run, the kinet

Re: [gmx-users] microcanonical

Well, I am back. Remember my first and second mdruns. In my second, after stablizing my initial configuration in the 1st md run, I used cut off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite large a distance compared to 0.309.  In the second run, the kinetic energy increases which

Re: [gmx-users] microcanonical

karamyog singh wrote: I know where the minimum is and I said exactly what you did. However I interpreted the potential becoming 0 as the point before r-min. The potential once becomes 0 before minimum potential value. I thought you were referring to that point and that is why i got confused and

Re: [gmx-users] microcanonical

I know where the minimum is and I said exactly what you did. However I interpreted the potential becoming 0 as the point before r-min. The potential once becomes 0 before minimum potential value. I thought you were referring to that point and that is why i got confused and asked you further questio

Re: [gmx-users] microcanonical

karamyog singh wrote: I placed the atoms randomly means i used random atomic positions, not velocities. The velocities were 0 initially and then I generated velocities at 0.01 K.(1st MD run to get a stable configuration) After that I subjected this structure that I got to NVE.(2nd MD run) Now o

Re: [gmx-users] microcanonical

I placed the atoms randomly means i used random atomic positions, not velocities. The velocities were 0 initially and then I generated velocities at 0.01 K.(1st MD run to get a stable configuration) After that I subjected this structure that I got to NVE.(2nd MD run) Now over here I will try with n

Re: [gmx-users] microcanonical

karamyog singh wrote: I exactly did that. I initially thought that since I have placed the atoms randomly so it is probable that atoms experience large forces and since I am not allowing any temperature scaling etc. , I am getting large KE. Therefore I first minimized my configuration. I got a

Re: [gmx-users] microcanonical

I exactly did that. I initially thought that since I have placed the atoms randomly so it is probable that atoms experience large forces and since I am not allowing any temperature scaling etc. , I am getting large KE. Therefore I first minimized my configuration. I got a frozen structure by doing

Re: [gmx-users] microcanonical

karamyog singh wrote: I almost removed everything. I am generating initial velocity at 0.01 K so the system should freeze. Its a dilute gas. But somehow I am getting very large velocites i.e. very large KE of the whole system. That .mdp looks fine for NVE. Use g_energy -w to see the evolution

Re: [gmx-users] microcanonical

I almost removed everything. I am generating initial velocity at 0.01 K so the system should freeze. Its a dilute gas. But somehow I am getting very large velocites i.e. very large KE of the whole system. here is my .mdp file. --- integrator   = md t

Re: [gmx-users] microcanonical

karamyog singh wrote: my system is simple gas and is interacting under simple LJ potential. isn't there a simpler way to do a simulation for a constant energy mode? It doesn't get any more simple than "don't do anything"! In gromacs, something approximating NVE is the result of doing nothing.

Re: [gmx-users] microcanonical

my system is simple gas and is interacting under simple LJ potential. isn't there a simpler way to do a simulation for a constant energy mode? i can remove pressure couling and temp. coupling. what kind of rigorous bond constraint algos do you mean? can you throw some more light on this topic? th

Re: [gmx-users] microcanonical

karamyog singh wrote: dear gromaxers.. how do i simulate a system under constant energy mode. Don't perturb the energy that is, don't use temperature or pressure regulation and use rigorous bond constraint algorithms. Be aware that use of cut-offs is inherently non-conservative of energy.

[gmx-users] microcanonical

dear gromaxers.. how do i simulate a system under constant energy mode. thanking you guys in advance. - karamyog. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques