Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-06-03 Thread Adam Herbst
...@fc.up.pt gyorgy.han...@fc.up.pt *To:* gmx-users@gromacs.org *Sent:* Thu, April 7, 2011 6:50:37 PM *Subject:* Re: [gmx-users] Is there still interest in rigid-body simulation? Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-04-07 Thread gyorgy . hantal
Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems with constraining some species in my simulations. Finally I've sorted out with shake but your solution seems to me less problematic. Thanks in advance. Best, Gyorgy Quoting ms

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-04-07 Thread Semen Esilevsky
...@fc.up.pt gyorgy.han...@fc.up.pt To: gmx-users@gromacs.org Sent: Thu, April 7, 2011 6:50:37 PM Subject: Re: [gmx-users] Is there still interest in rigid-body simulation? Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-04-07 Thread Justin A. Lemkul
-users@gromacs.org *Sent:* Thu, April 7, 2011 6:50:37 PM *Subject:* Re: [gmx-users] Is there still interest in rigid-body simulation? Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems with constraining some species in my simulations

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-04-07 Thread Luca Bellucci
Hi Adam, because some time ago I was involved in a rigid-body MD project, I am interested to known if you are following a published or known method. I do not know your rigid-body algorithm, however I would suggest you to take care on rotations, because they are not a simple task. Good luck

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-04-01 Thread mohsen ramezanpour
Welcome :) It is absolutely useful. On Mon, Mar 28, 2011 at 2:32 AM, Adam Herbst ad...@cornell.edu wrote: Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-03-28 Thread Ignacio Fernández Galván
From: Adam Herbst ad...@cornell.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, 28 March, 2011 0:02:17 Subject: [gmx-users] Is there still interest in rigid-body simulation? Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom

Re: [gmx-users] Is there still interest in rigid-body simulation?

2011-03-28 Thread ms
On 27/03/11 23:02, Adam Herbst wrote: Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it working for translational forces (not rotation, though this should be

[gmx-users] Is there still interest in rigid-body simulation?

2011-03-27 Thread Adam Herbst
Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it working for translational forces (not rotation, though this should be simple to add), even when the group is