[gmx-users] empty velocity *.xvg file from g_traj

Good morning! Firstly, I'd like to thank congratulate everyone involved for ver 4.0 Now for business: I'm getting empty *.xvg files from g_traj... this doesn't always happen, and I can't find what I'm doing differently... I'm running version 3.3.3 on Ubuntu:

Re: [gmx-users] density graph ( density vs time)

huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of

Re: [gmx-users] density graph ( density vs time)

huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? You could extract the box vectors with g_energy and compute the density from the volume. Best, Jochen Thanks.

[gmx-users] dielectric coffiecient

Deat justin thanks for your help. I delete cl- from (peptide,tfe ,water) in my system and I see about his charge not get message. when I add tfe in peptide (pdb2gmx -f name.pdb -ter -ignh )the lysin amino acid is protonated (2 lysin).another charge aminoacid is D,E.do you think it related to

[gmx-users] dihedrals again

Hi all, I did some work on thise dihedrals for polystyrene, and I simplified my version now, using also the inspiration from PHE residue. My problem now is that for the dihedral around the CH2-CH bond in the inner monomer (PS thus) I define in the rtp -CH CH2 CH +CH2gd_17 but

[gmx-users] Re: dihedrals again

Remark: if I change that dihedral with -CHCH2 CH CBgd_17, that it gives again 2 9 10 11 , but this time with gd_17, as it should do. But why it does not work with the other definition? Does it have to do with the fact that in the dihedral I have atoms belonging to 3

Re: [gmx-users] dielectric coffiecient

shahrbanoo karbalaee wrote: Deat justin thanks for your help. I delete cl- from (peptide,tfe ,water) in my system and I see about his charge not get message. when I add tfe in peptide (pdb2gmx -f name.pdb -ter -ignh )the lysin amino acid is protonated (2 lysin).another charge aminoacid is

Re: [gmx-users] Adding Na ions to DPPG

On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Peyman Yamin wrote: On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should

Re: [gmx-users] density graph ( density vs time)

huan wrote: Dear all, Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. So now i wonder is it there is another way that we can use other way to obtain a density (y axis) versus time length (x-axis). Use g_energy. -Justin Thanks.. --- On

Re: [gmx-users] density graph ( density vs time)

I used g_energy before but i just obtained density (y-axis) versus box length (x axis). now i wish to obtain density vs time thanks --- On Tue, 10/28/08, Justin A. Lemkul [EMAIL PROTECTED] wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] density graph ( density vs

Re: [gmx-users] density graph ( density vs time)

huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) thanks --- On Tue, 10/28/08,

Re: [gmx-users] density graph ( density vs time)

Jochen Hub wrote: huan wrote: I used g_energy before but i just obtained density (y-axis) versus box length (x axis). huan wrote: Previously i obtained a density (y-axis) versus box length (x axis) using g_density.. Sounds like a contradition to me... :-) Indeed; the

[gmx-users] table use

Hi all users, When I input the mdrun -table table_nonbond.xvg it always shows that : Fatal error: Library file tablep.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Has anyone encountered the same problem? Can you

[gmx-users] Is there any realation between structure and RMSD?

Hi all I have simulated two systems(mutated and unmutated)of protein for 7ns and I plotted RMSD. here my doubt is that when I see these structures(superimpose)in VMD mutated final simulated structure with respective initial one drastic changes(means helix-coil and Beta-alpha transitions) but

Re: [gmx-users] cannot generate .top file

Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even after i had added

Re: [gmx-users] cannot generate .top file

Kwee Hong wrote: Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the output files produced. I just added 'sudo' before ./pdb2gmx and it allows me to write in the directory. But unfortunately, this step seem does not work for ./gmxtest.pl. I'm having the same output even

[gmx-users] distance restraint

Dear gmx's user, May I asked you some technicl Questions? Do you know how to make distance restraint in gromacs? what I did I have created file name disre.itp as shown below [ distance_restraints ] ;   ai    aj type index type low up1 up2 fac    489   1133   1   1 1   0.25 0.35 0.40 1.0   

Re: [gmx-users] cannot generate .top file

Oo.. I'm so sorry for I'm not aware of this. But I'm really new to linux environment and don't really have a good mastering skill on the commandline that it works with. As you said that I'm not given the permission to write in that directory, sudo was the only thing that I can think of out from my