Re: [gmx-users] Re: charmm, cmap and gromacs 4.1

stefhoor wrote: Hi, > Hello. Thank you for the git repository tip, but I don't think it worked > out. > I tried using "git clone git://git.gromacs.org/gromacs.git ". Did you do git pull? > From the > gromacs directory

[gmx-users] Re: charmm, cmap and gromacs 4.1

Hi, > > > Hello. Thank you for the git repository tip, but I don't think it worked > > out. > > I tried using "git clone git://git.gromacs.org/gromacs.git". > > Did you do git pull? > > > From the > > gromacs directory that git created I ran "./bootstrap" and then > ./configure > > .etc. > > >

Re: [gmx-users] about the traj modification

You may first use make_ndx to create the index file then use trjconv to save the sub-system. On Jan 12, 2010, at 7:14 PM, zh.li wrote: > Dear all, > > I want to remove the water molecules in the original traj file (run.xtc) > to save the space, so that I should use the command “trjconv”.

Re: [gmx-users] about the traj modification

zh.li wrote: Dear all, I want to remove the water molecules in the original traj file (run.xtc) to save the space, so that I should use the command “trjconv”. But I don’t know which sub-command I should use to realize that? Does anyone here know how to do it?　Thank you very much.

[gmx-users] about the traj modification

Dear all, I want to remove the water molecules in the original traj file (run.xtc) to save the space, so that I should use the command “trjconv”. But I don’t know which sub-command I should use to realize that? Does anyone here know how to do it?　Thank you very much. Zhenwei Li --

Re: [gmx-users] distance from solute atom to the edge of the box

Oh. You are correct. I've gotten a little rusty. Thanks! On Tue, Jan 12, 2010 at 9:10 AM, Justin A. Lemkul wrote: > > > Arden Perkins wrote: > >> Also, you can type " -h " in your terminal and it will bring up a list >> of commands and options for the program and can usually explain what they

Re: [gmx-users] SiO2 simulation

Hi, As far as I know, you must build the structure file by yourself, and the topology file. For the force field, the SiO2 have been included in the ffG53a6 and opls force field. However, it seems that the LJ parameters of Si in both of them is inconsistent with the original publication. rega

Re: [gmx-users] distance from solute atom to the edge of the box

Arden Perkins wrote: Also, you can type " -h " in your terminal and it will bring up a list of commands and options for the program and can usually explain what they mean/do. For example: -h pdb2gmx Such a command is incorrect. The -h flag must follow the Gromacs tool, otherwise you wi

Re: [gmx-users] SiO2 simulation

Arden Perkins wrote: I believe pdb files (protein data bank) are only for peptides, so unless you are simulating a peptide you will not need any pdb files for your There are numerous utilities that generate .pdb files; it is not true to say that .pdb files only contain proteins/peptides. A

Re: [gmx-users] distance from solute atom to the edge of the box

Also, you can type " -h " in your terminal and it will bring up a list of commands and options for the program and can usually explain what they mean/do. For example: -h pdb2gmx Arden Perkins On Tue, Jan 12, 2010 at 4:17 AM, leila karami wrote: > Hi > > How is determined distance from solute at

Re: [gmx-users] SiO2 simulation

I believe pdb files (protein data bank) are only for peptides, so unless you are simulating a peptide you will not need any pdb files for your SiO2. Your structure file (.gro) for SiO2 may be in the fftw library files (or whatever forcefield you're using). Hope that helps. Arden Perkins On Tue, J

Re: [gmx-users] charmm, cmap and gromacs 4.1

Hi, > Hello. Thank you for the git repository tip, but I don't think it worked > out. > I tried using "git clone git://git.gromacs.org/gromacs.git". Did you do git pull? > From the > gromacs directory that git created I ran "./bootstrap" and then ./configure > .etc. > I inserted the ffcharm

[gmx-users] Re: charmm, cmap and gromacs 4.1

> > Hi Stefan, > > > Message: 2 > > Date: Mon, 11 Jan 2010 19:48:53 -0200 > > From: Stefan Hoorman > > Subject: [gmx-users] charmm, cmap and gromacs 4.1 > > To: gmx-users@gromacs.org > > Message-ID: > > <3078c1dd100348m6fb3d96epcc9202869d7b3...@mail.gmail.com> > > Content-Type: text/plai

Re: [gmx-users] hydrogen bond

leila karami skrev: Hi I want to obtain following parameters about water molecule and hydrogen bonds in pr-dna simulation: 1) residence time of number of water mediated hydrogen bonds 2) life time of number of water mediated hydrogen bonds 3) number of water mediated hydrogen bonds 4)

[gmx-users] hydrogen bond

Hi I want to obtain following parameters about water molecule and hydrogen bonds in pr-dna simulation: 1) residence time of number of water mediated hydrogen bonds 2) life time of number of water mediated hydrogen bonds 3) number of water mediated hydrogen bonds 4) number of direct hydrogen bo

RE: [gmx-users] Triggering generic kernel causes LINCS warnings

Hi, My answer was nonsense. The fix I saw was from 2008, not 2009. With water you need GMX_NO_SOLV_OPT together with GMX_NB_GENERIC. Berk > Date: Tue, 12 Jan 2010 13:26:22 +0100 > Subject: RE: [gmx-users] Triggering generic kernel causes LINCS warnings > From: pvant...@xs4all.nl > To: gmx-user

Re: [gmx-users] distance from solute atom to the edge of the box

I just answered this message several minutes ago. Please do not double-post. http://lists.gromacs.org/pipermail/gmx-users/2010-January/048019.html -Justin leila karami wrote: -- Forwarded message -- From: *leila karami* > Date: Tue, Jan 12,

[gmx-users] distance from solute atom to the edge of the box

-- Forwarded message -- From: leila karami Date: Tue, Jan 12, 2010 at 3:47 PM Subject: distance from solute atom to the edge of the box To: gmx-users@gromacs.org Hi How is determined distance from solute atom to the edge of the box in editconf command (what criterion)? Any hel

Re: [gmx-users] charmm, cmap and gromacs 4.1

Hi Stefan, > Message: 2 > Date: Mon, 11 Jan 2010 19:48:53 -0200 > From: Stefan Hoorman > Subject: [gmx-users] charmm, cmap and gromacs 4.1 > To: gmx-users@gromacs.org > Message-ID: > <3078c1dd100348m6fb3d96epcc9202869d7b3...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-

RE: [gmx-users] Triggering generic kernel causes LINCS warnings

Hi Berk, Thanks for your quick answer. Are the modifications done only in nb_generic.c, so I could 'patch' my altered version of 4.0.5? Pieter > > Hi, > > This is a bug which I fixed in 4.0.7 (but somehow it is missing from the > revision list). > > Berk > >> Date: Tue, 12 Jan 2010 12:11:23 +01

Re: [gmx-users] binding affinity

leila karami wrote: Hi I want to compare DNA-binding affinity of PRH protein by mutation of some aminoacids. I think KD (dissociation constant) is related to binding affinity. I dont know how do I obtain KD (dissociation constant) by MD simulation and gromacs (what command). There isn

Re: [gmx-users] distance from solute atom to the edge of the box

leila karami wrote: Hi How is determined distance from solute atom to the edge of the box in editconf command (what criterion)? http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin Any help will highly appreciated! -- ==

[gmx-users] distance from solute atom to the edge of the box

Hi How is determined distance from solute atom to the edge of the box in editconf command (what criterion)? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

RE: [gmx-users] Triggering generic kernel causes LINCS warnings

Hi, This is a bug which I fixed in 4.0.7 (but somehow it is missing from the revision list). Berk > Date: Tue, 12 Jan 2010 12:11:23 +0100 > From: pvant...@xs4all.nl > To: gmx-users@gromacs.org > Subject: [gmx-users] Triggering generic kernel causes LINCS warnings > > Hello, > > I'm trying to

[gmx-users] SiO2 simulation

Dear all I am a new user of Gromacs. I am interested to simulate amorphous SiO2 and I would like to know if someone can send me the .pdb and .top files. Thanks in advance Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Triggering generic kernel causes LINCS warnings

Hello, I'm trying to simulate a water box with protein and drug. Having set up the simulation, starting mdrun causes no problems on its own. However, after setting the GMX_NB_GENERIC environment variable and restarting the simulation, it crashes at step 20 with too many LINCS warnings. Disabeling

[gmx-users] binding affinity

Hi I want to compare DNA-binding affinity of PRH protein by mutation of some aminoacids. I think KD (dissociation constant) is related to binding affinity. I dont know how do I obtain KD (dissociation constant) by MD simulation and gromacs (what command). If there is another way, please guide m