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. Viswa

[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 Intern

[gmx-users] Problems in bonded parameters for nitrate with OPLS in GROMACS

Hi GMXers I'm trying to use in my simulations the nitrate ion defined in OPLS (ffoplsaa.atp) force field as atom-types opls_787 and opls_788, but when I look at OPLS bonded parameters in ffoplsaabon.itp I can't find bonds, angles or dihedral parameters with it's bond_type (N and O as defined in f

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] 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

Dear Mark I read the manual but I could not find any option to get the original values of the matrix. I will be highly appreciative if you can help. thanks Ninoo Mani --- Mark Abraham <[EMAIL PROTECTED]> wrote: > > Dear all > > > > I run g_rms with -m option that produces a matrix > in > > .xpm

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 wa

[gmx-users] Fatal error: Shake block crossing node boundaries

Hi GMX-Users, I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting topology... Walking down the molecule graph to make shake-blocks There are 24390 charge group b

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

[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] 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 http://www.gromacs.org/mailman/listinfo/gmx-

[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] distance restraints: -merge

From: "Owen, Michael" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: 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 specific atoms of a protein. I recently

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 g_rota

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 of