Re: [gmx-users] Magnetic field in GROMACS

2018-06-21 Thread حبيبة علي
Dear Alex, Thanks for your words. Yes, we have going on research and we look to the future. But we are suffering from the lack of resources. We did some work on electric field code but we could not call the velocity of each particle to do the cross product with the magnetic field and also our cod

Re: [gmx-users] Magnetic field in GROMACS

2018-06-21 Thread Alex
I would at least first try to hardcode a test Lorentz force for e.g. a given constant magnetic field to see what happens and whether you can observe anything fun. On an unrelated note, I just want to say that it is great to see that there is scientific research going on in Iraq after years of

Re: [gmx-users] Magnetic field in GROMACS

2018-06-21 Thread حبيبة علي
I thought you are a developer ;) I think updating electric field file is not a problem but the complicated thing is what are the other files that related to it. Such as how to implement it in mdp files which I think need to update different files. If there are any analyzing commands need updating,

Re: [gmx-users] Magnetic field in GROMACS

2018-06-21 Thread Alex
Nah, I'm just a user. ;) What David and I were discussing is not a beginner's task (and I can't see a large number of users for that otherwise awesome functionality), but if you'd like to code the simple vector product, I am pretty sure there will be those who could direct you to the right fil

Re: [gmx-users] Magnetic field in GROMACS

2018-06-21 Thread حبيبة علي
Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahme

Re: [gmx-users] Magnetic field in GROMACS

2018-06-20 Thread Ali Ahmed
Hello, I looked for that before and I tried updating the electric field code as both of them are related to Lorentz force. Unfortunately, I failed because there are different codes need to be updated. It would be amazing if the developers participate in this code. Thanks Ali On Wed, Jun 20, 2018 a

Re: [gmx-users] Magnetic field in GROMACS

2018-06-20 Thread David van der Spoel
Den 2018-06-20 kl. 10:20, skrev Alex: David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorent

Re: [gmx-users] Magnetic field in GROMACS

2018-06-20 Thread Alex
David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorentz force applied to point charges would

Re: [gmx-users] Magnetic field in GROMACS

2018-06-20 Thread David van der Spoel
Den 2018-06-20 kl. 09:26, skrev حبيبة علي: Dear Dr. David, I'm Habiba, I just start learning GROMACS and I'm going to apply magnetic field on my system which is polymer. I looked online then I noticed its not implemented in GROMACS but, people are talking about it. You shared all GROMACS packa