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, a

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 th

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

__ > From: gmx-users-boun...@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] Co

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 http://l

[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 the

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 > solve

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

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 > > ../m

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

w3.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 On Wed, 28 Apr 2010 13:35:31 -0400, Justin A. Lemkul wrote > J. Rui Rodrigues wrote: > >

[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 confi

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 tra

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

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