Re: [gmx-users] problem with total energy

Dear Mark and Justin, Thanks for your help, as a beginner to GROMACS i think i have to spend even more time with each option and make sure i know what i am doing. I will spend some time by using different electrostatic options with out pbc and let you know what happens to the simulations. Thanks

Re: [gmx-users] problem with total energy

On 9/04/2010 1:25 PM, jampani srinivas wrote: Dear Justin, I am sorry for the poor description of the problem, OK let me explain you clearly here. I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain rad

Re: [gmx-users] problem with total energy

Dear Justin, I am sorry for the poor description of the problem, OK let me explain you clearly here. I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain radius (in this case it is 2.5 nm). To achieve t

Re: [gmx-users] problem with total energy

jampani srinivas wrote: Dear Justin, Thanks for your responce. Here is my mdp file. +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.004 ; ps ! nsteps = 2500 ; t

Re: [gmx-users] problem with total energy

Dear Justin, Thanks for your responce. Here is my mdp file. +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.004 ; ps ! nsteps = 2500 ; total 100.0 ns. nstcomm

Re: [gmx-users] problem with total energy

jampani srinivas wrote: Hi Thanks for your response, I am allowing the two groups (frozen and non-frozen) groups interact each other, i guess i am getting the energy of total system from g_energy. I checked the velocities of frozen group atoms, they are not "zero". I have seen in git mas

Re: [gmx-users] problem with total energy

Hi Thanks for your response, I am allowing the two groups (frozen and non-frozen) groups interact each other, i guess i am getting the energy of total system from g_energy. I checked the velocities of frozen group atoms, they are not "zero". I have seen in git master that this problem was fixed a

Re: [gmx-users] problem with total energy

jampani srinivas ha scritto: > Dear Berk, > > I am sorry if i am confusing you with my poor description of problem, > actually I have submitted simulation with two temperature coupling groups (i > think you already know that from our earlier conversations) and found that > there is a continuous in

[gmx-users] problem with total energy

Dear Berk, I am sorry if i am confusing you with my poor description of problem, actually I have submitted simulation with two temperature coupling groups (i think you already know that from our earlier conversations) and found that there is a continuous increase in the total energy of the system.