Re: 回复： Re: 回复： Re: [gmx-users ] Is 2D projection in g_anaeig

xi zhao wrote: Dear sir: I am sorry. Can I understand 2D projection = Probability Distributions P(v1,v2) in Proteins 2005; 60:485. How to produce 3D Don't know the paper, but such a projection can give you a probability distribution if you histogram it. plot of P(v1,v2)? how can I look

Re: [gmx-users] gromacs-3.3.1 installation problem

Chenyue Xing wrote: Hi all, I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1 with --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and lib/ directories. ./configure successfully passed all checking (seems so) but it stopped at ' config.status: executing

Re: [gmx-users] comm_mode

[EMAIL PROTECTED] wrote: Dear users, There is an option in .mdp named comm_mode, which deals with the transition and rotation of the molecule being simulated. I want to know why the transition and rotation happens during the simulation. Can any one suggest me any reading material where in I

Re: [gmx-users] gromacs-3.3.1 installation problem

Hi David, Thanks for your reply. I actually found the time difference (25 min different)between my working machine and the other machine where files are. I'll contact my sysadmin. But as I successfully installed gromacs-3.1 under the same condition, does that mean this problem only occurs on

Re: [gmx-users] gromacs-3.3.1 installation problem

Chenyue Xing wrote: Hi David, Thanks for your reply. I actually found the time difference (25 min different) between my working machine and the other machine where files are. I'll contact my sysadmin. But as I successfully installed gromacs-3.1 under the same condition, does that mean this

[gmx-users] Uncorrelated configurations

Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? Thanks eef

Re: [gmx-users] Uncorrelated configurations

Eudes Fileti wrote: Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? what is the

RE: [gmx-users] AFM pulling

From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer

[gmx-users] entries in ffG53a6nb.itp

dear all// what is the meaning of and the difference between the [ nonbond_params ] and the [ pairtypes ] sections in the ffG53a6nb.itp file? represents the first the normal LJ-params while the latter contains the 1-4 interaction LJ-params? what is the meaning of 'ptype' and 'func' in the

[gmx-users] contact

Dear gromacs users How can i calculate the number of contacts during the MD trajectory in complex(protein-protein)? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

RE: [gmx-users] AFM pulling

Thanks, that's good to know! Susanna From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the

Re: [gmx-users] entries in ffG53a6nb.itp

On Aug 14, 2006, at 2:49 PM, Carsten Baldauf wrote: dear all// what is the meaning of and the difference between the [ nonbond_params ] and the [ pairtypes ] sections in the ffG53a6nb.itp file? represents the first the normal LJ-params while the latter contains the 1-4 interaction

Re: [gmx-users] histidine (HISB) planarity how about Trp?

Hi everybody, I am also trying G53a6 in my protein simulation and it is observed that TRP is less planar as compared to those in OPLS. The angle distribution of the impropers are calculated to be wider and thus less populated in the equilibrium angle. Would this hint to a problem in the setup

[gmx-users] Re: gmx-users Digest, Vol 28, Issue 42

Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are structural and statistically not correlated. For this, up to now, I

Re: [gmx-users] Re: gmx-users Digest, Vol 28, Issue 42

Eudes Fileti wrote: Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. sorry, I don't memorize it all... Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are

[gmx-users] The file

HI! I have a problem. I am working with a molecule that will count two clusters, co-ordinated for cysteins. But in the pdb file does not exist linkings between iron atoms and of the cystens, even so literature affirms that it exists. How I can edit this file? Therefore when I edited it even so

Re: [gmx-users] The file

Elias santos wrote: HI! I have a problem. I am working with a molecule that will count two clusters, co-ordinated for cysteins. But in the pdb file does not exist linkings between iron atoms and of the cystens, even so literature affirms that it exists. How I can edit this file?

[gmx-users] renumtop

Dear users Where I can find renumtop thank you prabhakaran ___ 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 or send it to

[gmx-users] nr2nametop

Dear users whwre I can get nr2nametop also and mainly renumtop thank you Prabhakaran ___ 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

[gmx-users] Sigh . . . Protonating PDB for PRODRG

Hey all, I'm trying to import energy minimization files into VMD to view and I'm getting some errors. First I note that: • small molecule pdb file shows a total of 48 atoms • my new molecule topology (*.itp file, and *.gro file) show 22 atoms, which I thought were