Re: [gmx-users] Amino acid simulation

It's highly unusual to simulate a single amino acid. I don't exactly know what's your purpose with it, but if you really want to do it, you need to generate those parameters. I know there are web services for generating gromos FF parameters for unusual molecules, possibly there are such resources

Re: [gmx-users] System has non-zero total charge: -8.000001e+00

You should always neutralise your sysem. On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo mauriciomr1...@gmail.com wrote: IS this a problem? *System has non-zero total charge: -8.01e+00* If yes, can I fix that changing COulomb cutt-off to PME electrostatics? THanks!! --

[gmx-users] genbox

Is it possible to maximise the water molecules to be inserted into the box? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] special molecule

What I asked is, if I have to reorganise the pdb file, or renumber the residues, etc.On 6/13/06, Mark Abraham [EMAIL PROTECTED] wrote:Tamas Horvath wrote: So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?The

Re: [gmx-users] special molecule

Does it mean, that the itp file, generated by the PRODRG server should only used with the gmx forcefield, or may it be combined with the other gromos frocefields, like the G43a2?On 6/13/06, Mark Abraham [EMAIL PROTECTED] wrote: Dongsheng Zhang wrote: Sear Mark, Since PRODRG server only generates

[gmx-users] special molecule

As I understand, if there are special molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I

Re: [gmx-users] special molecule

PRODRG? In another word, can I mix two different force field (one for protein, one for ligand) in one system? Thanks! Best Wishes! Dongsheng On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham wrote: Tamas Horvath wrote: As I understand, if there are special molecules in a pdb file, pdb2gmx

Re: [gmx-users] Imaging in PBC simulations

I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.On 4/24/06, Martin LEPSIK [EMAIL PROTECTED] wrote:Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best wayto image a