[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e

Re: [gmx-users] (no subject)

hazizian wrote: Subject: protein domain separate Date: Mon, 19 Oct 2009 08:56:36 +0430 Message-Id: <20091019042502.m55...@razi.tums.ac.ir> X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi

[gmx-users] (no subject)

Subject: protein domain separate Date: Mon, 19 Oct 2009 08:56:36 +0430 Message-Id: <20091019042502.m55...@razi.tums.ac.ir> X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi Tsjerk where shoul

Re: [gmx-users] Protein Orientation

sure. thanks On Sun, Oct 18, 2009 at 10:45 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: >> >> oh cool. I have gromacs version 4.4 so my protein will be on the x >> axis by default and to orient the long axis of protein along z axis >> then I have to editconf it and then rotate the final

Re: [gmx-users] Protein Orientation

sunny mishra wrote: oh cool. I have gromacs version 4.4 so my protein will be on the x axis by default and to orient the long axis of protein along z axis then I have to editconf it and then rotate the final structure to 90 degrees along y axis, right? reply will be highly appreciated Try it

Re: [gmx-users] Protein Orientation

oh cool. I have gromacs version 4.4 so my protein will be on the x axis by default and to orient the long axis of protein along z axis then I have to editconf it and then rotate the final structure to 90 degrees along y axis, right? reply will be highly appreciated Thanks, Sunny On Sun, Oct 18,

Re: [gmx-users] Protein Orientation

sunny mishra wrote: Dear All, I am following the tutorial given by justin and have question regarding the orientation of protein. Tutorial says that orient the protein along z axis using editconf -princ command followed by the rotation along y axis. My question is that when I use the editconf

[gmx-users] Protein Orientation

Dear All, I am following the tutorial given by justin and have question regarding the orientation of protein. Tutorial says that orient the protein along z axis using editconf -princ command followed by the rotation along y axis. My question is that when I use the editconf -princ command, does it

[gmx-users] Check out my photos on Facebook

Hi gmx-users@gromacs.org, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Jack To sign up for Facebook, follow the lin

Re: [gmx-users] How to let Gromacs run 60% faster..

Vaclav Horacek wrote: Hello, I just bumped into the site www.yasara.org, who claims that their just released new MD algorithms are 60% faster then Gromacs. Actually they dont say 'Gromacs', but 'closest competitor', which I assume is Gromacs looking at the benchmark numbers. One should alway

[gmx-users] NPE simulations: where does all the energy go?

Dear colleagues, There is probably some stupidity involved in my question, but I want to use GROMACS to explore water phase equilibria using the phase coexistence technique. This means that my simulation cell contains a liquid slab and an ice slab in contact, and what I'm trying to do is to see wh

Re: [gmx-users] protein domain separate

Hi, You have to use -pbc nojump with a _suitable_ reference. Cheers, Tsjerk On Sun, Oct 18, 2009 at 11:59 AM, hazizian wrote: > Hi again > I use -pbc mol -ur compact but the problem still exist. > > > -- > Tehran University of Medical Sciences > www.tums.ac.ir > > > -- > This message has been

[gmx-users] protein domain separate

Hi again I use -pbc mol -ur compact but the problem still exist. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users ma

Re: [gmx-users] force field

leila karami wrote: I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. For AMBER, downlo

Re: [gmx-users] protein domain separation

Vaclav Horacek wrote: Hi Hazizian, I have done md simulation of a 2-domain protein in water, in 50 K but every time I did it these domains are separated from each other, and dont correct when I do trjconv -pbc nojump, This also happened to me once, since it can be impossible to correct t

[gmx-users] force field

I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. ___

[gmx-users] How to let Gromacs run 60% faster..

Hello, I just bumped into the site www.yasara.org, who claims that their just released new MD algorithms are 60% faster then Gromacs. Actually they dont say 'Gromacs', but 'closest competitor', which I assume is Gromacs looking at the benchmark numbers. >From the numbers, I also saw that they s

Re: [gmx-users] protein domain separation

Hi Hazizian, > I have done md simulation of a 2-domain protein in water, > in 50 K but every > time I did it these domains are separated from each other, > and dont correct > when I do trjconv -pbc nojump, This also happened to me once, since it can be impossible to correct the trajectory wit

[gmx-users] force field

there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. ___ gmx-users mailing listgmx-users@groma

[gmx-users] protein domain separation

Hi I have done md simulation of a 2-domain protein in water, in 50 K but every time I did it these domains are separated from each other, and dont correct when I do trjconv -pbc nojump, previous time when I did em or pr by doing trjconv -pbc nojump, it corrected. The 50.mdp file is: title

Re: [gmx-users] number of opposition ions

leila karami wrote: Dear Mark Abraham you said me For neutralization of system and understanding the number of ions with opposition (pr + dna), pdb2gmx or grompp will probably report net charges if non-zero. what file exactly reports net charge? The on-screen output. Do read it - it's us

[gmx-users] number of opposition ions

Dear Mark Abraham you said me For neutralization of system and understanding the number of ions with opposition (pr + dna), pdb2gmx or grompp will probably report net charges if non-zero. what file exactly reports net charge? ___ gmx-users mailing list