Re: [gmx-users] Coarse Grained force field

2008-09-06 Thread Myunggi Yi
Dear users, I found MARTINI CG force fields. http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html On Thu, Sep 4, 2008 at 3:14 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Thu, 4 Sep 2008 14:59:55 -0400 > "Myunggi Yi" <[EMAIL PROTECTED]> wrote: > >> Dear gmx users, >> >> I'd like to r

[gmx-users] Re[6]: Using Morse potentials with ENCAD force field

2008-09-06 Thread Vitaly Chaban
AS> The system works now, thanks for finding a simple mistake.  Another question I had is if I want to calculate the average velocities of all the atoms over a period of time can I use g_traj to create an average velocity of the atoms, but looking at all_veloc.xvg file the atom number starts a

[gmx-users] g_energy

2008-09-06 Thread Alessandro . Maiorana
Hi, how does it count the drift in g_energy? What is the equation? What is the difference among fluct. and RMSD? Thanks, see you soon. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] printing coords ; energies

2008-09-06 Thread Omer Markovitch
Thank you. Sorry for not being clearer. I meant where in the source code are the energy related functions & variables? Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 16:19, Jochen Hub <[EMAIL PROTECTED]> wrot

Re: [gmx-users] Harmonic distance restraint during simulation

2008-09-06 Thread Justin A. Lemkul
Manoj Kumar Singh wrote: What if I want to restrain distance between two different molecules. I tried this and getting error. I looked at some previous posts and didn't find any solution to this. Some of them say it is limitation of Gromacs. Since distance restraints are added to the topol

Re: [gmx-users] Harmonic distance restraint during simulation

2008-09-06 Thread Xavier Periole
On Sat, 06 Sep 2008 06:13:35 -0400 "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Manoj Kumar Singh wrote: What if I want to restrain distance between two different molecules. I tried this and getting error. I looked at some previous posts and didn't find any solution to this. Some of them s

Re: [gmx-users] Coarse Grained force field

2008-09-06 Thread Xavier Periole
On Sat, 6 Sep 2008 04:59:54 -0400 "Myunggi Yi" <[EMAIL PROTECTED]> wrote: Dear users, I found MARTINI CG force fields. That is the best choice you could make! :)) http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html Then dig a bit in the website and you'll find everything to start a simula

Re: [gmx-users] g_energy

2008-09-06 Thread ravi sharma
Hi, RMSD is your just deviation of backbone from native stare while RMS fluctuation shows the per atom deviation throughout simulation. regards, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut

[gmx-users] trr file format

2008-09-06 Thread Vitaly Chaban
Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,&fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Thanks. -- Vitaly

Re: [gmx-users] trr file format

2008-09-06 Thread David van der Spoel
Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,&fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :