Re: [gmx-users] Force fields, is there a review article?

nteresting (just found googling the title of other papers I have just listed): http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf Regards. L -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale "Jean-Pierre Ebel" UMR 5075 CNR

[gmx-users] Identical energies generated in a rerun calculation ... but ...

re likely a code bug ... but I wait for your comments and/or suggestions. Thanx in advance Luca _______ Luca Mollica Biomolecular NMR Laboratory 1B4 Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute Via Olgetti

[gmx-users] urea topology for MARTINI (CGMD)

ers, Luca -- .... -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com) Telephone: +33.438783889 -- Elwood: It's 106 m

Re: [gmx-users] urea topology for MARTINI (CGMD)

On 05/11/2010 04:57 PM, XAvier Periole wrote: On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote: If we follow strictly the parameterization guides, these are only guide lines ... no need to follow "strictly" :)) Actually this was the problem: CG seems easy because of a reduced n

Re: [gmx-users] asking help for simulation of protein in 8M urea

So ... what's your goal ? :) At the moment I am too working on some systems that require the usage of urea and doing a bit of set up for AMBER FF, whereas in the past I have used a topology for the last GROMOS FF. Cheers Luca -- .......

Re: [gmx-users] Essential Dynamics

molecular dynamics simulations were decomposed into essential motions for the first time". I don't know if it's suitable for beginners or not: for sure it represents the begin of the story ... :) Luca -- ........ -- Luca Mol

Re: [gmx-users] Essential Dynamics

s.org/Documentation/How-tos/Essential_Dynamics L -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 38027 France E-mail: luca.moll...@ibs.fr (lucamoll...@gmai

Re: [gmx-users] stepsize too small ... but potential energy negative!

annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you're too small to make a change, try sleeping with a mosquito" -- -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut

Re: [gmx-users] stepsize too small ... but potential energy negative!

a.htm "If you think you're too small to make a change, try sleeping with a mosquito" -- ........ -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale 41 Rue Jules Horowitz Grenoble 380

Re: [gmx-users] stepsize too small ... but potential energy negative!

- my system is a protein (with or w/o ligand) in solvent (water SPC). Following your suggestions, I tried to perform an EM on the protein w/o ligand after the editconf step (i.e. I created the topology with pdb2gmx, created a cubic box with editconf, then I used grompp+mdrun to perform EM). I

Re: [gmx-users] stepsize too small ... but potential energy negative!

= inf Anna Message: 2 Date: Fri, 21 May 2010 14:44:04 +0200 From: Luca Mollica Subject: Re: [gmx-users] stepsize too small ... but potential energy negative! To: Discussion list for GROMACS users Message-ID:<4bf68014.1060...@ibs.fr> Content-Type: text/plain; charset

[gmx-users] PME usage in 3.3 & g_energy: doubt ?

Luca :::::: Luca Mollica Dulbecco Telethon Institute c/o DIBIT - S. Raffaele Scientific Institute Biomolecular NMR Laboratory, 1B4 Via Olgettina 58 20132 Milano Italy Tel: 00390226433497 Fax: 00390226434153 An expert is a man who has made all the mistakes which can be made in a narrow field. (

Re: [gmx-users] PME usage in 3.3 & g_energy: doubt ?

First, with rlist = rvdw, you will not get long range Lennard Jones interactions. In fact I would recommend using a larger vdw cut-off, as 0.9 is very short. Are you sure you are using the same mdp file? Yes it is and I have used the standard values suggested by GROMACS guide. (3.2 and 3.

[gmx-users] Zn ion as a metal center in a protein: setting distance restraints

Dear all, I have tried to simulate my protein-ligand system in water as usual, but my protein has two Zn atoms that bind 3Cys and 1 His (Zn1) and 4Cys (Zn2). I have browsed the literature and the ML: the most common suggestion that I had found was the usage of distance restraints in my protein

Re: [gmx-users] Lipid Bilayer Simulations

Hi Mike! > I am new to Gromacs, and I am working with > lipid bilayer simulations. > I am attempting to just run an energy minimization > on a lipid bilayer so I > can get a better feel for the program. I have taken > the files dppc128.pdb, > dppc.itp, lipid.itp and example2.itp from Peter

[gmx-users] glutathionylation and SS bonds formation in GMX

of the same molecule, actually. But I cannot get the point for this failure in the system building process. Thanks in advance & Bye LM ___ Luca Mollica Biomolecular NMR Laboratory 1B4 Dulbecco Telethon Institute c/o S. Raff