Re: [gmx-users] Problem installin gmx

On 13/02/10 15:29, Chandan Choudhury wrote: What is a cross-compiler? One that compiles an executable for architecture other than the one on which compilation occurs. My system is x86_64 x86_64 x86_64 GNU/Linux model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz vendor id: GenuineIn

Re: [gmx-users] Problem installin gmx

What is a cross-compiler? My system is x86_64 x86_64 x86_64 GNU/Linux model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz vendor id: GenuineIntel Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham wrote: > > > On 02/13/10, *Chandan Choudhur

Re: [gmx-users] Problems wtih g_wham

Jennifer Casey wrote: Hello, I am trying to create a PMF for the sodium cation and iodine anion in the presence of THF. I have been following the umbrella sampling tutorial on the gromacs website, and everything has been working out. I have finally created 14 different equilibriation simu

[gmx-users] Problems wtih g_wham

Hello, I am trying to create a PMF for the sodium cation and iodine anion in the presence of THF. I have been following the umbrella sampling tutorial on the gromacs website, and everything has been working out. I have finally created 14 different equilibriation simulations, whose starting confi

Re: [gmx-users] Latest gmxtest in git

On 02/13/10, Jess Bromley wrote:> I haven't actually run 4.0.7 against git gmxtest, but I made the last commit> to the latter, and it was routine for correctly-functioning 4.0.x versions> to fail the tests you mention. I think your installation is fine.Thanks Mark, that's very encouraging!Just a

Re: [gmx-users] problem normal mode analysis

On 02/13/10, sarbani chattopadhyay wrote:hi, I want to do a normal mode analysis on a small peptide. I had complied gromacs in double precision and energy minimized the structure in vacuum, using steepest descent followed by conjugate gradient method. the log file of conjugate gradient metho

Re: [gmx-users] Problem installin gmx

On 02/13/10, Chandan Choudhury wrote:Hello gmx users !!I installed successfully installed fftw. Then tried compiling gmx parallely I executed the command $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ It didnot show any problem. $makemake[5]: Entering directory `/home/vanka/NUM-GE

Re: [gmx-users] Latest gmxtest in git

> Just a quick followup: when I run the tests in parallel mode I'm also > seeing checkvir related failures in complex/field (~250-275 errors) > and complex/tip4flex (1 or 2 errors), although strangely the latter > PASSES for 4 CPUs and fails for other numbers.  Is this kind of > behaviour also expe

Re: [gmx-users] Latest gmxtest in git

> I haven't actually run 4.0.7 against git gmxtest, but I made the last commit > to the latter, and it was routine for correctly-functioning 4.0.x versions > to fail the tests you mention. I think your installation is fine. Thanks Mark, that's very encouraging! Just a quick followup: when I run t

[gmx-users] Re: problems with intel I7 (2.67 GHz)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello everybody. I would like to chime in here also my problem might not be directly related. > The problem of Gromacs stalling on i7 when using multiple CPUs is a MPI > problem. It is most likely caused by a shared memory bug in Open MPI > that wa

[gmx-users] Problem installin gmx

Hello gmx users !! I installed successfully installed fftw. Then tried compiling gmx parallely I executed the command $ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/ It didnot show any problem. $make make[5]: Entering directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonde

[gmx-users] problem normal mode analysis

hi, I want to do a normal mode analysis on a small peptide. I had complied gromacs in double precision and energy minimized the structure in vacuum, using steepest descent followed by conjugate gradient method. the log file of conjugate gradient method reads Polak-Ribiere Conjugate Gradient

Re: [gmx-users] problems in setup the protein+ membrane

Thanks for Your suggestion, I will use an updated forcefield & gradually adjust each error lines. Jit On Fri, Feb 12, 2010 at 6:50 PM, Justin A. Lemkul wrote: > > > chiloo777 777 wrote: >> >> So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as >> following lines. >> Please sugge

Re: [gmx-users] problems in setup the protein+ membrane

chiloo777 777 wrote: So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as following lines. Please suggest me, how can i remove such errors. Well, an arbitrary change to a deprecated force field just to get around a simple atom type mismatch may or may not be the best way to

Re: [gmx-users] problems in setup the protein+ membrane

So, I've changed forcefield from ffG53a6 to ffgmx, the errors are as following lines. Please suggest me, how can i remove such errors. Thanks Jit Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for inter