Re: [gmx-users] Entropy from NMA

Dear Ran and Nahren, I run into a similar problem a couple of weeks ago: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html In short, integrator = steep can be run in parallel. Output from parallel and single-node are equal. integrator = l-bfgs runs only in single-node, as

Re: [gmx-users] scripting question

google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the

Re: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] Compiling problems on MacOS X 10.6.4

...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx- users] Compiling problems on MacOS X 10.6.4 Hi, Please post the output of the following

[gmx-users] parallel run with integrator=nm ?

Dear all, In an attempt to speed up things, I tried to calculate an hessian matrix in parallel, using two processors and it finished in about half the time when compared to a single-node run. However, the parallel run produces an .mtx file that has about half the size of the one obtained in

Re: [gmx-users] acetonitrile from amber to gromacs

Hi, You could use acpype, although you will need to push more than one button :-) http://code.google.com/p/acpype/ Cheers, Rui Rodrigues On Wed, 19 May 2010 18:15:29 +0200, vedat durmaz wrote hi all together, this week i'm trying to do some simulations with acetonitrile (AN) as a solvent

Re: [gmx-users] question about installing gromacs on a mac

Hi, I have never tried to compile gromacs with MKL, but you could try to configure with CFLAGS=-framework mkl Hope this helps, Rui Rodrigues On Wed, 5 May 2010 12:15:23 -0400, Emily Curtis wrote I apologize in advance if this is a very stupid question. I am trying to configure GROMACS on

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

Hi, (...) Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno- unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la

[gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve performance. With gromacs-4.0.7, the option --enable-apple-64bit of configure has disappeared and

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

On Wed, 28 Apr 2010 13:35:31 -0400, Justin A. Lemkul wrote J. Rui Rodrigues wrote: Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve

Re: [gmx-users] Handling modified residue

Jiang, pdb2gmx first looks for files in your working directory, and then in gromacs directory. Hope this helps, Rui Rodrigues On Sat, 14 Nov 2009 12:05:04 -0500, Jiang Zhu wrote Dear all, I have been a GROMACS user for some time but this is my first time to handle a modified

Re: [gmx-users] Trajectory files in vmd

Dear Aditi, What do you mean with evolution of the protein structure? Are you referring to *secondary structure*? By default, VMD only calculates it for the first trajectory frame. --Rui On Thu, 24 Sep 2009 10:51:04 +0530, Aditi Borkar wrote Dear All, When I am loading the GROMACS

RE: [gmx-users] gromacs on glacier.westgrid.ca

Hi, On Tue, 19 May 2009 14:23:07 -0600, Payman Pirzadeh wrote Hi Justin, Following is the script I use. But remember several points: ${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest You have a dot before /global/...

Re: [gmx-users] dssp install problems

Hi, Try this: cd /usr/local/bin sudo ln -s dsspcmbi dssp Hope this help, Rui Rodrigues On Fri, 3 Apr 2009 13:44:56 -0400, KS Rotondi wrote All, I've looked at the site and cannot figure this out, so apologies if this is a painful often seen question. I'm trying to install dssp for

Re: [gmx-users] Can not open file: topol.tpr

It's not mdrun -v deffnm em, but: mdrun -v -deffnm em Rui On Tue, 03 Mar 2009 15:52:36 +0300, drugdesign wrote Oh, I am very sorry, I've copied the wrong error. Actually error was with the same tutorial at the next step with mdrun -v deffnm em. I can't figure out why I need topol.tpr