[gmx-users] (no subject)

Dear gmx-users, I have a rather elementary question regarding the value of box vectors when invoked by g_energy. If I am shearing a system using deform option, what does exactly, say, "Box-XY" represent? Thanks, gc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] deform option

Hi, I posted this question earlier but no-one answered it to me so I am going to ask this question again. On deform option in .mdp file, what is being done if you are shearing the system? i.e., if I do: deform = 0 0 0 1 0 0 it seems to change box-xy value. but what does it mean? thanks, gc --

[gmx-users] Best Minimization Protocol for given protein

ients or L-BFGS?, emtol= ?, solvated or vacuum?)? Thanks in advance, Russell Green ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before po

[gmx-users] dihedral .ndx format

each, but could someone kindly show me an example format? Thanks, Russell Green ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Pl

[gmx-users] dPCA "atoms"

elping to define the dihedral angles. Could someone please provide some suggestions or more insight? I've searched the net and the mailing list but have found no information regarding my question. Thanks in advance, Russell Green UAB Undergraduate Researcher

Re: [gmx-users] dPCA "atoms"

Thanks Yang Ye! I will look into this further. Thanks for the program, I'm sure that will save me much time. Russell Green On 6/11/07, Yang Ye <[EMAIL PROTECTED]> wrote: As what we normally do with dPCA, after obtaining the 2D projection of first and second principle, we make i

[gmx-users] pdb2gmx not recognizing disulfides

Hello, I'm having problems with pdb2gmx not recognizing disulfides in my protein. I've tried chaning the residue name and -ss flag but neither works. I read that this was a known bug on the website. Does anyone have a fix for this? Thanks, Rus

Re: [gmx-users] pdb2gmx not recognizing disulfides

disulfide bonds. And, if I use higher bond lengths the number of disulfide CYS found decreases. Where should I look next to sort out this problem? Thanks, Russell Green On 7/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Did you use specbond.dat correctly? http://wiki.gromacs.org/ind

Re: [gmx-users] pdb2gmx not recognizing disulfides

ase, you have to use the option -merge with pdb2gmx. pdb2gmx will not usually make bonds between different chains. Hope this helps, Tsjerk On 7/1/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Russell Green wrote: > > Hello, > > > > I just changed the disulfide max b

Re: [gmx-users] pdb2gmx not recognizing disulfides

y. So should I still be doing something different other than my idea to change the residue names of the .itp files, as mentioned previously? Sorry for some of my ignorance, I'm still new with much of this. Thanks for all the suggestions and input! Thanks, Russell Green On 7/2/07, David van

Re: [gmx-users] pdb2gmx not recognizing disulfides

e with S-S bonds, and you get that by producing one by hand or using pdb2gmx. Could you or anyone else point me in the right direction to do this? Again, thanks for all the help and insight. Russell Green ___ gmx-users mailing listgmx-users@gromac

Re: [gmx-users] pdb2gmx not recognizing disulfides

s with the chains. When I use the -ignh option, all the cysteines are protonated (which is not what should be happening). If I use the -ss option...nothing happens. Sorry for the late reply, Russell Green On 7/2/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Thanks for the tip. I didn't t

[gmx-users] Fwd: project 4

-- Forwarded message -- From: Wasef Muzaffar <[EMAIL PROTECTED]> Date: Oct 8, 2007 1:03 AM Subject: Fwd: project 4 To: Russell Green <[EMAIL PROTECTED]> -- Forwarded message -- From: Wasef Muzaffar <[EMAIL PROTECTED]> Date: Oct 17, 2006 10

[gmx-users] ascii Covariance matrix

ear how this is done. I would like to do this using the data from the ascii file. If anyone could explain this to me, or tell me were to look, I would really appreciate it. Thanks in advance, Russell Green ___ gmx-users mailing listgmx-us

[gmx-users] Need basic install help please

le Gromacs and it appeared to compile. However, when I type in a command, I get the bash command not found message. What am I doing wrong? Did I compile it incorrectly? Am I missing a step? Thank you, Russell Green ___ gmx-users mailing listgmx-users@g

Re: [gmx-users] Need basic install help please

I don't think the scripts were in my path...but I tried chaning the .bash_profile with no luck. I'm in the /home/local directory and my gromacs directory is in there too. Is there a way I can check to see if gromacs is actually on the system? Thanks, Russell Green On 2/8/07, Dallas

Re: [gmx-users] Need basic install help please

n the home/russell/ directy as I have it? Thanks, Russell Green On 2/9/07, Dallas B. Warren <[EMAIL PROTECTED]> wrote: Type "which mdrun". That should return to tell you if that script is within your path. If it returns that it isn't, then you need to find where GROMACS

Re: [gmx-users] Need basic install help please

Oh...I see. I will try that. I'm re-compiling it just to make sure everything is at default. Thanks On 2/9/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Russell Green wrote: > Pardon my ignorance of Linux...but after remembering I did the standard > install I went searching fo

Re: [gmx-users] Need basic install help please

Ok...I tried the find command and it tells me there's no such file or directory?? Now I really don't know what to do. Russell Green On 2/9/07, Russell Green <[EMAIL PROTECTED]> wrote: Oh...I see. I will try that. I'm re-compiling it just to make sure everything is at def

Re: [gmx-users] Need basic install help please

PATH=$PATH:/usr/local/gromacs/bin/GMXRC followed by export=PATH. I tried GMXRC' and GMXRC.bash but nothing happens still. ??? Thanks, Russell Green On 2/9/07, Russell Green <[EMAIL PROTECTED]> wrote: Ok...I tried the find command and it tells me there's no such file or directory

Re: [gmx-users] Need basic install help please

OOh...my apologies Mark. I completely missed the 'source... part for the path. Please forgive my annoyances...it's late and I was getting really frustrated. Well I've shut down the computer for now because I need some sleep, but I'll try what you said exactly tomorrow. Thank you Mark and everyone