Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Mark Abraham
On Wed, Jun 19, 2013 at 10:30 AM, Steven Neumann wrote: > Why? To avoid refining and extrapolating 100 tables for a Coarse grained > run and use constants instead... I'd still think writing the script in your language of choice to write out the tables is a much lighter weight proposition than se

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Steven Neumann
Why? To avoid refining and extrapolating 100 tables for a Coarse grained run and use constants instead... And to make it faster obviously. On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham wrote: > No. You're modifying the C code, so you will have to learn to maintain > a GROMACS installation. Yet a

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Mark Abraham
No. You're modifying the C code, so you will have to learn to maintain a GROMACS installation. Yet another reason to avoid modifying the C code :-) Mark On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann wrote: > I will speak to someone who is familiar with the code. However, my Gromacs > version

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Mark Abraham
On Wed, Jun 19, 2013 at 9:41 AM, Steven Neumann wrote: > On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote: > >> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann > >wrote: >> >> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote: >> > >> > > >> > > >> > > On 6/10/13 5:16 AM, Steven Neumann w

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Steven Neumann
I will speak to someone who is familiar with the code. However, my Gromacs version is installed on the cluster, can I create a file in my directory which will use this code with a given potential? On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann wrote: > > > > On Tue, Jun 18, 2013 at 6:07 PM, Mar

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-19 Thread Steven Neumann
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote: > On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann >wrote: > > > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote: > > > > > > > > > > > On 6/10/13 5:16 AM, Steven Neumann wrote: > > > > > >> Thank you. > > >> Do you know whether it is poss

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-18 Thread Mark Abraham
On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann wrote: > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote: > > > > > > > On 6/10/13 5:16 AM, Steven Neumann wrote: > > > >> Thank you. > >> Do you know whether it is possible to use the 5th order polynomial for > >> angles in Gromacs? I know I c

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-18 Thread Justin Lemkul
On 6/18/13 11:39 AM, Steven Neumann wrote: On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote: On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-18 Thread Steven Neumann
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote: > > > On 6/10/13 5:16 AM, Steven Neumann wrote: > >> Thank you. >> Do you know whether it is possible to use the 5th order polynomial for >> angles in Gromacs? I know I can use tables but wish to fit my data into >> such a function. >> >> > No

Re: [gmx-users] Quartic Angle

2013-06-12 Thread Steven Neumann
The constant angle has a weird units of kJ /mol rad^n while the angle is in degrees. Does not make sense but at least I know where I made a mistake... On Wed, Jun 12, 2013 at 10:43 PM, Justin Lemkul wrote: > > > On 6/12/13 10:01 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> I run a simul

Re: [gmx-users] Quartic Angle

2013-06-12 Thread Justin Lemkul
On 6/12/13 10:01 AM, Steven Neumann wrote: Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight)

[gmx-users] Quartic Angle

2013-06-12 Thread Steven Neumann
Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight). I have in my topology [ angles ] ; i j k

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-10 Thread Justin Lemkul
On 6/10/13 5:16 AM, Steven Neumann wrote: Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Nothing in the manual seems to suggest that such a form is supported. -Justin

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-10 Thread Steven Neumann
Thank you. Do you know whether it is possible to use the 5th order polynomial for angles in Gromacs? I know I can use tables but wish to fit my data into such a function. Steven On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul wrote: > > > On 6/5/13 8:40 AM, Steven Neumann wrote: > >> Dear Gmx Us

Re: [gmx-users] Quartic angle potential - how to use?

2013-06-05 Thread Justin Lemkul
On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed b

[gmx-users] Quartic angle potential - how to use?

2013-06-05 Thread Steven Neumann
Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user