Re: [gmx-users] Gromacs 4 with mpi interface

On Thu, 2008-12-18 at 01:03 +0530, Chitrita Dutta Roy wrote: > Can anyone give me a detailed notes on how to install gromacs 4 with > mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as > i am new to using gromacs plz give me as detailed note as possible.. Just install using yum:

Re: [gmx-users] Gromacs 4 with mpi interface

Hi, Please don't "top post", particularly when responding to multiple topics in one email, as it makes it hard for people to understand the context of your remarks. A better approach is to insert new paragraphs after the text you refer to. You can also appear to be a more credible source of g

Re: [gmx-users] Gromacs 4 with mpi interface

U just have to modify the .top file, Just add the line "Na+ 2" at the bottom of the file where u can find "SOL "and also u have to substract 2 from the SOL number. Thats it. Regarding MPI, if u r using MULTIPLE MACHINESthen MPI is useful otherwise , if u r using single machine wit

[gmx-users] Re[2]: What water topology is worth using?

Hi Dimitry, D> field I`m using. Can I use spc with OPLS AA? I think you can. As for me when simulating water I prefer SPC/E but it's only my personal taste. Best, Vitaly D> Thank you for answering. D> Nevertheless I believe that each model is based on appropriate force D> field. As I learned

Re: [gmx-users] What water topology is worth using?

Thank you for answering. One more question. As I learned spc is for use with GROMOS and tip3p - with OPLS AA. I use OPLS AA. Should I consider using tip3p or it does not really matter? Thank you. On Wed, 2008-12-17 at 19:41 +0100, Xavier Periole wrote: > On Wed, 17 Dec 2008 20:55:28 +0300 > Di

[gmx-users] RE: Gromacs 4 with mpi interface

> Can anyone give me a detailed notes on how to install gromacs 4 with mpi > feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new > to using gromacs plz give me as detailed note as possible.. The most primitive way would be probably ./configure --enable-mpi make make install

[gmx-users] RE: What water topology is worth using?

> what solvent topology do you use in your simulations? I`ve always used > spc and had no problems with it. Though recently I`ve heard that tip3p > is better. What do you suggest? What do you use? I think it much depends on what exact properties you calculate. You may calculate something very spec

Re: [gmx-users] Gromacs 4 with mpi interface

From genion -h: "genion replaces solvent molecules by monoatomic ions at the position of the first atoms with the most favorable electrostatic potential or at random." That would explain how genion works, and what you must do to update the topology correctly. If you have added 2 NA+, then you

Re: [gmx-users] Gromacs 4 with mpi interface

What exactly Do we need to change in the topology file suppose if we add 2 NA+ ions in the system..??? On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul wrote: > > > Chitrita Dutta Roy wrote: > >> Can anyone give me a detailed notes on how to install gromacs 4 with mpi >> feature..I am using Int

Re: [gmx-users] Gromacs 4 with mpi interface

Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. Installation instructions are on the Gromacs webpage and

[gmx-users] Gromacs 4 with mpi interface

Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. And after adding some ions using genion when i try to run grompp again before final mdrun

Re: [gmx-users] What water topology is worth using?

On Wed, 17 Dec 2008 20:55:28 +0300 DimitryASuplatov wrote: Hello, what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? Don't worry this comment was probabl

[gmx-users] What water topology is worth using?

Hello, what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? Thanks SDA ___ gmx-users mailing listgmx-users@groma

Re: [gmx-users] Free energy of transfer with accuracy

Eudes, > But first I would want to know two things. > 1) The parameter sc-sigma of 0.5 is reasonable? > How this parameter affects the shape of dvdl plot? > You performed tests about it? I found little about > it in the forum. Check out the manual on what this parameter does. IIRC it only applies

Re: [gmx-users] Free energy of transfer with accuracy

Chris, > "Also, if your C60 is hollow, I can imagine that it might > exclude solvent atoms from the inside, in which case you are going to > have a big convergence issue as solvent begins to interpenetrate with > the C60, which may lead to "noise" problems when this starts to > happen, whatever so

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

Hi Berk, thanks for the trick. Unfortunately I'm not in my lab right now and can't open easily xterms over the network. I'll try to catch up once I'm back (end of December), unless Bernhard or Antoine find the solution. Cheers, Patrick Berk Hess a écrit : Hi, You can do something like: mpi