Re: [gmx-users] OpenMosix and Gromacs

On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote: > > I wonder if someone has some experience with Gromacs and OpenMosix. Has > someone tried recently to run Gromacs in parallel with an OpenMosix > cluster? I have read some messages about that on the mailing-list but I have not tr

Re: [gmx-users] OpenMosix and Gromacs

Hi, On Jul 2, 2007, at 11:15 AM, Ansgar Esztermann wrote: On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote: I wonder if someone has some experience with Gromacs and OpenMosix. Has someone tried recently to run Gromacs in parallel with an OpenMosix cluster? I have read some mes

[gmx-users] Dismantling the methyl group

Hi, I've run into problems with simulating a methanol - water system. My purpose is to do an electronic structure calculation for configurations generated with Gromacs, however the thing is that Gromacs handles the methyl group as a single unit whereas I need the coordinates of the carbon and of

Re: [gmx-users] Dismantling the methyl group

Hi Jussi, Gromacs only handles the methyl as a single particle if you tell it to, i.e. by taking a united atom force field like GROMOS. You can use OPLS/Amber in stead. Of course you can add the hydrogens based on an ideal geometry for each frame, but I think you'll miss part of the points of gen

Re: [gmx-users] Dismantling the methyl group

Hi, You should use an all-atom force field. I assume you're using one of the Gromos force fields, which is of united-atom type. /Erik 2 jul 2007 kl. 12.27 skrev Jussi Lehtola: Hi, I've run into problems with simulating a methanol - water system. My purpose is to do an electronic structu

[gmx-users] S-S Bonds

Dear GROMACS Users, I want to do MD of insulin monomer (first two chain of 4ins.pdb). When I convert with pdb2gmx, the software find only one ss bond (the only inside the same chain). I have resolved this problem doing a first conversion pdb->gro, then gro->pdb end in the final conversion

Re: [gmx-users] S-S Bonds

Hi Roberto, I want to do MD of insulin monomer (first two chain of 4ins.pdb). When I convert with pdb2gmx, the software find only one ss bond (the only inside the same chain). I have resolved this problem doing a first conversion pdb->gro, then gro->pdb end in the final conversion pdb->gro the s

Re: [gmx-users] Dismantling the methyl group

Hi again, thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have a .gro file (& al) for methanol using OPLS or another all-hydrogen force field? I tried running pdb2gmx on the tutorial .pdb files, but it failed with the error Fatal error: Atom Me1 in residue MET 1 not found in

Re: [gmx-users] Dismantling the methyl group

Jussi Lehtola wrote: Hi again, thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have a .gro file (& al) for methanol using OPLS or another all-hydrogen force field? I tried running pdb2gmx on the tutorial .pdb files, but it failed with the error Fatal error: Atom Me1 in res

Re: [gmx-users] Dismantling the methyl group

2 jul 2007 kl. 14.32 skrev David van der Spoel: Jussi Lehtola wrote: Hi again, thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have a .gro file (& al) for methanol using OPLS or another all-hydrogen force field? I tried running pdb2gmx on the tutorial .pdb files, but it

[gmx-users] trajconv

Hi all I am new to Gromacs: I am simulating pure polymer (22 monomers and 16 linear chains) in vaccum and i have a few questions regarding the trjconv command. I run a NPT simulation for 500 picosecond and when i see the output (.gro) file in vmd i found some holes my simulation box. I mean 2 or

Re: [gmx-users] trajconv

Hi Ann, I run a NPT simulation for 500 picosecond and when i see the output (.gro) file in vmd i found some holes my simulation box. I mean 2 or 3 chains were away from the center position of the box where other chains were residing. so i thought of performing a NVT simulation follwed by BD for

[gmx-users] Applying constant force between two atoms

Dear gmx-users, I want to apply constant force between two atoms within a protein. But unfortunately I cannot find how to apply constant force. Would anybody talk me how to do it? Thanks, Seungpyo ___ gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Applying constant force between two atoms

> Dear gmx-users, > > > > I want to apply constant force between two atoms within a protein. > > But unfortunately I cannot find how to apply constant force. > > Would anybody talk me how to do it? Probably not, but if you read Chapters 3-5 of the manual, you will see some ideas that are probably

Re: [gmx-users] pdb2gmx not recognizing disulfides

Hmm...well the thing is, I just need a .tpr file (which I was getting with pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to xtc format. The simulation is already complete, I'm just converting it, but of course the atoms from the tpr need to match those of the trajectory. So

Re: [gmx-users] pdb2gmx not recognizing disulfides

Russell Green wrote: Hmm...well the thing is, I just need a .tpr file (which I was getting with pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to xtc format. The simulation is already complete, I'm just converting it, but of course the atoms from the tpr need to match thos

Re: [gmx-users] pdb2gmx not recognizing disulfides

> Hmm...well the thing is, I just need a .tpr file (which I was getting with > pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to > xtc > format. The simulation is already complete, I'm just converting it, but of > course the atoms from the tpr need to match those of the trajec

Re: [gmx-users] pdb2gmx not recognizing disulfides

If you are using trjconv, a gro or pdb can be fed to -s option. tpr is not necessary. Regards, Yang Ye On 7/2/2007 10:01 PM, Russell Green wrote: Hmm...well the thing is, I just need a .tpr file (which I was getting with pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to

Re: [gmx-users] Dismantling the methyl group

Can you figure out which type of atom is this Me1? Regards, Yang Ye On 7/2/2007 8:45 PM, Erik Marklund wrote: 2 jul 2007 kl. 14.32 skrev David van der Spoel: Jussi Lehtola wrote: Hi again, thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have a .gro file (& al) for metha

Re: [gmx-users] Dismantling the methyl group

On Mon, 2007-07-02 at 23:08 +0800, Yang Ye wrote: > Can you figure out which type of atom is this Me1? > > Regards, > Yang Ye It is the methyl group, CH_3. -- Mr. Jussi Lehtola Research Assistant Division of Theoretical Physics / Division of High Energy Physics IT services Department of Physica

Re: [gmx-users] [Fwd: How simulate two peptides in a box?]

Hello Gromacs users: I am running a dimeric protein simulation on Gromacs 3.3 using the force filed G43a1. For initially minimizing the hydrogen i did some small minimization and equilibration in the vacuum by maintaining the restraints then i added ions and water but in the very first minimi

Re: [gmx-users] pdb2gmx not recognizing disulfides

Thanks for the tip. I didn't think to try it. But if I plan to do any electrostatics I still need the tpr file right? So I would need to produce a top file. Mark, you mentioned making the S-S bonds by hand. You still won't get them bonded with this procedure... you need a .top file with S-S bond

[gmx-users] What is the box type of output files?

Dear all, I am new to Gromacs, and I am trying to simulate my systems with octahedral box type (the option I used for editconf was "-bt octahedral"). I need to know what type of box that Gromacs put the output systems in, because I am trying to do some translations on some molecules that are outs

Re: [gmx-users] What is the box type of output files?

On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote: Dear all, I am new to Gromacs, and I am trying to simulate my systems with octahedral box type (the option I used for editconf was "-bt octahedral"). I need to know what type of box that Gromacs put the output systems in, because I am trying to do some

[gmx-users] which tpr?

Hello all, Because of the limitations in run time, my simulations have broken into three parts: one.trr, two.trr, and three.trr. Each run has its corresponding tpr file. The original tpr file (minimization step) was start.tpr. Now using trjconv for three.trr which tpr file I need to type after -s

Re: [gmx-users] which tpr?

Terry Nelson wrote: Hello all, Because of the limitations in run time, my simulations have broken into three parts: one.trr, two.trr, and three.trr. Each run has its corresponding tpr file. The original tpr file (minimization step) was start.tpr. Now using trjconv for three.trr which tpr fil

Re: [gmx-users] What is the box type of output files?

Thank you very much, it is very helpful for me. nslam Yang Ye <[EMAIL PROTECTED]> wrote: On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote: > Dear all, > > I am new to Gromacs, and I am trying to simulate my > systems with octahedral box type (the option I used > for editconf was "-bt octahedral"). > I n

Re: [gmx-users] pdb2gmx not recognizing disulfides

> Thanks for the tip. I didn't think to try it. But if I plan to do any > electrostatics I still need the tpr file right? So I would need to produce > a > top file. Mark, you mentioned making the S-S bonds by hand. You can see that trjconv doesn't really need a .tpr because trjconv -h shows you th

Re: [gmx-users] which tpr?

> Hello all, > > Because of the limitations in run time, my simulations have broken into > three parts: one.trr, two.trr, and three.trr. Each run has its > corresponding > tpr file. The original tpr file (minimization step) was start.tpr. Now > using > trjconv for three.trr which tpr file I need to

Re: [gmx-users] Applying constant force between two atoms

Thank you for paying attention. Maybe I have to study much more about Gromacs. ^^; Seungpyo On 7/2/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Dear gmx-users, > > > > I want to apply constant force between two atoms within a protein. > > But unfortunately I cannot find how to apply constant

Re: [gmx-users] [Fwd: How simulate two peptides in a box?]

> Hello Gromacs users: Please don't reply to another user's question with a change of topic and not change the subject line of your email. Not doing this means the people who might know the answer for you have no idea in advance what you're going to be asking, and might not bother reading. Best i

[gmx-users] g_wham and PMF problem

Hey All, I am trying to use g_wham command to compute PMF.Can anyone please let me know how to use that command? When I try giving the input files sequentially like g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo, there is an error message saying, that it is not a valid input file forma

Re: [gmx-users] g_wham and PMF problem

> Hey All, > I am trying to use g_wham command to compute PMF.Can anyone please let > me know how to use that command? Well there's g_wham -h and the section on WHAMin the manual... > When I try giving the input files sequentially like > > g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo

[gmx-users] How to get ligand top file for oplsaa?

Dear all, I have a ligand molecule, and I want to get its opls all-atom force field topology file. How can I get it? I don't know how to establish the atom types and the charge of the ligand. Any reply will be appreciated. sincerely Rui Li ___ gmx-use

Re: [gmx-users] which tpr?

Hey :) Errm, trjconv does read coordinates, so when using -fit or -pbc nojump, the results will depend on the structure file used. Tsjerk On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Hello all, > > Because of the limitations in run time, my simulations have broken into > three parts: o

Re: [gmx-users] How to get ligand top file for oplsaa?

Hi Rui Li, See http://wiki.gromacs.org/index.php/Parameterization Tsjerk On 7/3/07, Rui Li <[EMAIL PROTECTED]> wrote: Dear all, I have a ligand molecule, and I want to get its opls all-atom force field topology file. How can I get it? I don't know how to establish the atom types and the charg

Re: [gmx-users] g_wham and PMF problem

Hey Mark, Appreciate your immediate response.You can find the input and the error below: g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo pull5.pdo :-) g_wham (-: Option Filename Type Description --

Re: [gmx-users] which tpr?

> Hey :) > > Errm, trjconv does read coordinates, so when using -fit or -pbc > nojump, the results will depend on the structure file used. > > Tsjerk > > On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote: >> trjconv just needs any old structure file. You can see this if you >> follow >> my suggesti

Re: [gmx-users] g_wham and PMF problem

> Hey Mark, > Appreciate your immediate response.You can find the input and > the > error below: > g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo pull5.pdo g_wham -h suggests that -hist won't accept multiple input files. Only a few GROMACS utilities will do magic concate