Re: [gmx-users] NMA for a group

2007-06-25 Thread Lars Schaefer
Christian Seifert wrote: On Friday 22 June 2007 11:22, Lars Schaefer wrote: Hi Christian, I am not sure what exactly you need the Hessian for. But if you are interested in IR spectra, you might also calculate them from dipole autocorrelation (instead of from the hessian). Best, Lars You ar

Re: [gmx-users] NMA for a group

2007-06-25 Thread David van der Spoel
Christian Seifert wrote: On Friday 22 June 2007 11:22, Lars Schaefer wrote: Hi Christian, I am not sure what exactly you need the Hessian for. But if you are interested in IR spectra, you might also calculate them from dipole autocorrelation (instead of from the hessian). Best, Lars You are ri

Re: [gmx-users] NMA for a group

2007-06-25 Thread Christian Seifert
On Friday 22 June 2007 11:22, Lars Schaefer wrote: > Hi Christian, > I am not sure what exactly you need the Hessian for. But if you are > interested in IR spectra, you might also calculate them from dipole > autocorrelation (instead of from the hessian). > Best, > Lars You are right. We are inter

Re: [gmx-users] NMA for a group

2007-06-22 Thread Nguyen Hoang Phuong
Hi Christian, Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the hessian just for the phosphate. How do I do that? I have done something similar like what you want to do. I calculate t

Re: [gmx-users] NMA for a group

2007-06-22 Thread Bert de Groot
Mark Abraham wrote: > Christian Seifert wrote: >> On Friday 22 June 2007 10:59, Bert de Groot wrote: > >> The hessian is the second (numerical) derivative of the atoms in the >> three dimensions. In the future, I want to calculate the hessian of >> molecules next to proteins, so the "small droplet

Re: [gmx-users] NMA for a group

2007-06-22 Thread Mark Abraham
Christian Seifert wrote: On Friday 22 June 2007 10:59, Bert de Groot wrote: The hessian is the second (numerical) derivative of the atoms in the three dimensions. In the future, I want to calculate the hessian of molecules next to proteins, so the "small droplet of explicit water" will not wo

Re: [gmx-users] NMA for a group

2007-06-22 Thread David van der Spoel
Christian Seifert wrote: On Friday 22 June 2007 10:59, Bert de Groot wrote: David van der Spoel wrote: Christian Seifert wrote: Hi. Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the

Re: [gmx-users] NMA for a group

2007-06-22 Thread Christian Seifert
On Friday 22 June 2007 10:59, Bert de Groot wrote: > David van der Spoel wrote: > > Christian Seifert wrote: > >> Hi. > >> > >> Perhaps, I made a mistake in describing my problem. I can not believe, > >> that no one ever tried this before. > >> > >> I have a phosphate in water and want to calculate

Re: [gmx-users] NMA for a group

2007-06-22 Thread Bert de Groot
David van der Spoel wrote: > Christian Seifert wrote: >> Hi. >> >> Perhaps, I made a mistake in describing my problem. I can not believe, >> that no one ever tried this before. >> >> I have a phosphate in water and want to calculate the hessian just for >> the phosphate. How do I do that? > > ther

Re: [gmx-users] NMA for a group

2007-06-22 Thread Christian Seifert
On Friday 22 June 2007 11:07, Mark Abraham wrote: > David van der Spoel wrote: > > Christian Seifert wrote: > >> Hi. > >> > >> Perhaps, I made a mistake in describing my problem. I can not believe, > >> that no one ever tried this before. > >> > >> I have a phosphate in water and want to calculate

Re: [gmx-users] NMA for a group

2007-06-22 Thread Lars Schaefer
Hi Christian, I am not sure what exactly you need the Hessian for. But if you are interested in IR spectra, you might also calculate them from dipole autocorrelation (instead of from the hessian). Best, Lars Christian Seifert wrote: Hi. Perhaps, I made a mistake in describing my problem. I

Re: [gmx-users] NMA for a group

2007-06-22 Thread Mark Abraham
David van der Spoel wrote: Christian Seifert wrote: Hi. Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the hessian just for the phosphate. How do I do that? there is a contradicti

Re: [gmx-users] NMA for a group

2007-06-22 Thread David van der Spoel
Christian Seifert wrote: Hi. Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the hessian just for the phosphate. How do I do that? there is a contradiction here in that you say the

Re: [gmx-users] NMA for a group

2007-06-22 Thread Christian Seifert
Hi. Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the hessian just for the phosphate. How do I do that? Regards, Christian On Tuesday 19 June 2007 14:39, Christian Seifert wrote: >

[gmx-users] NMA for a group

2007-06-19 Thread Christian Seifert
Hi. I want to make a NMA just for one Group of molecules, because a QMMM-NMA takes too long for the whole system. Of cause, the EM in the step before has been done for the whole system. The manual does not tell how to do this. Did someone tried this before? Thanks Christian. -- B.Sc. Christ