Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs

Hi! You may want to try PLUMED, which is the evolution of grometa http://merlino.mi.infn.it/~plumed/PLUMED/Home.html and can do also steered MD and umbrella sampling. Massimiliano On Jan 27, 2010, at 8:48 AM, David van der Spoel wrote: On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote: Dear Dr.

Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs

Hi, LES as developed by Elber is available in CHARMM and MOIL. Ran. Massimiliano Bonomi wrote: Hi! You may want to try PLUMED, which is the evolution of grometa http://merlino.mi.infn.it/~plumed/PLUMED/Home.html and can do also steered MD and umbrella sampling. Massimiliano On Jan 27,

[gmx-users] J-walking REMD

Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this

Re: [gmx-users] Problems with gromacs-openMM

Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM, jorge_quint...@ciencias.uis.edu.co

Re: [gmx-users] J-walking REMD

You can try using the TEE-REX module, the GROMACS 3.3.x version has worked for me in the past on a system too large for standard REMD. Tom David Parcej wrote: Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST

[gmx-users] linking gromcs to efence

Hi, I am trying to link mdrun with efence, but don't really know how. I have been trying to add the -lefence to the CFLAGS or to the LDFLAGS, but that doesn't seem to work. Any help would be appreciated. Thanks in advance, Jochen -- --- Dr.

RE: [gmx-users] linking gromcs to efence

Hi, Why not use valgrind? I switched from efence to valgrind a long time ago. If you have a Mac it might be less effort to log into a linux machine and run valgrind there. Berk Date: Wed, 27 Jan 2010 17:32:07 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users]

Re: [gmx-users] linking gromcs to efence

Hi Jochen, it should work by putting it in the LDFLAGS. Either you should then get an executable that says something like Electric Fence 2.2.0 at the very start of execution or it should not compile when the library is not found. Carsten On Jan 27, 2010, at 5:32 PM, Jochen Hub wrote:

Re: [gmx-users] Potential Energy

I did not develop the force field of my molecule by myself. In stead I use the literature force field parameters. I guess not all the force field need the [pairs]. As long as I can get reasonable experimental observables, I can use such force field, right? On Tue, Jan 26, 2010 at 6:50 PM, Mark

[gmx-users] Gromacs commercial license

Hello folks!! Does anyone know if there is a GROMACS version to commercial use, or under somekind of license? If so, how should I proceed to get such license? Best regards!! -- Att. Guilherme Menegon Giesel -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Gromacs commercial license

On Wednesday 27 January 2010 19:40:57 Guilherme Menegon Giesel wrote: Hello folks!! Does anyone know if there is a GROMACS version to commercial use, or under somekind of license? If so, how should I proceed to get such license? Best regards!! Gromacs is under GPLv2 license

Re: [gmx-users] Gromacs commercial license

Gromacs is under GPLv2 license (http://www.gnu.org/licenses/gpl-2.0.html) and you can use it for commercial purpose without any problem. EXCEPT distributing new commercial binaries that use any of the Gromacs code, without also distributing the source for the code. (did I get all the GPL

[gmx-users] Questions about Pull Code

Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a trajectory of configurations along

Re: [gmx-users] Questions about Pull Code

Jennifer Casey wrote: Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a

[gmx-users] Genbox error message

Hello all, Can someone tell me the meaning of this error message after using the genbox command? *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map:

Re: [gmx-users] Genbox error message

On 28/01/10 13:06, Lum Nforbi wrote: Hello all, Can someone tell me the meaning of this error message after using the genbox command? Certainly not without more useful information - GROMACS version, simulation system size, actual command line. Even then, the best guess is probably that