Re: [gmx-users] Re: water molecules in vacuum simulation.

Hi Anwar, The constraints are defined in spc.itp (or any of the other water models). So if you use -DPOSRES they are included automatically. Best, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University

Re: [gmx-users] g_rotacf again

Hi Rama, You would be able to do it by taking one of two approaches: 1. Write the centers of masses and from this generate a multipdb file (or gro file) containing three atoms spanning two vectors perpendicular to the vector between these centers of masses. This trajectory can be used for

RE: [gmx-users] distance restraints: -merge

From: Owen, Michael [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] distance restraints: -merge Date: Tue, 26 Sep 2006 11:10:15 -0500 Fellow gmx-users, I would like to constrain the distance of an ion to

[gmx-users] contact

Dear freinds I want to analyz the formed contact in during the MD.How can i do with gromacs? best regard __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

Re: [gmx-users] contact

mahbubeh zarrabi wrote: Dear freinds I want to analyz the formed contact in during the MD.How can i do with gromacs? Read section 7.4 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_cluster -dm

Hello, I am trying to use g_cluster. However, the result I am obtaining when using a pre-calculated RMSD matrix with the -dm option is quite different than the one I get when the RMSD matrix is calculated by g_cluster from a trjectory of structures. Is this a matter of precision in the xpm

Re: [gmx-users] g_cluster -dm

Nikos Sgourakis wrote: Hello, I am trying to use g_cluster. However, the result I am obtaining when using a pre-calculated RMSD matrix with the -dm option is quite different than the one I get when the RMSD matrix is calculated by g_cluster from a trjectory of structures. Is this a matter

Re: [gmx-users] Free energy calculations

http://md.chem.rug.nl/education/Free-Energy_Course/index.html http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial Both very decent. Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR (USA) Viswanadham Sridhara wrote: Hello gmx-users, I

[gmx-users] gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2

Hi, all, Has anyone out there successfully compiled gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2 on a Bluegene server? I am not sure how the environment variables should be set. Your input would be much appreciated. Best wishes, Art

Re: [gmx-users] g_rms, matrix and raw data

Hi Ninoo, You can hack the code of gmx_rms.c in [GMXSRCDIR]/src/tools/ to output the matrix generated into a human readable format. It is also possible to write a raw binary file which can easily be processed using a scripting language such as python (use g_rms -bin). Best, Tsjerk On 9/27/06,

[gmx-users] density map

Hi, how can I get the number density values from g_densmap? I would like to play with these values, such as finding the points of greatest density, for instance. Regards. Pedro. This message was sent using IMP, the

Re: [gmx-users] Free energy calculations

Hi, the review by David Pearlman can be very useful in relation to FEP-type calculations o Free Energy Calculations: Methods for Estimating Ligand Binding Affinities Chapter 2 In: Free energy calculations in rational drug design M. Rami Reddy Mark D. Erion Eds. Best regards, Javier N.