Re: [gmx-users] Glycoproteion MD

2012-08-31 Thread Laercio Pol Fachin
Hi, If you can't find parameters for glycoprotein's MD for charmm27, OPLS or Amber99 (and GROMOS is an alternative for you), we've been working on MD simulations with this class of biomolecules, using GROMOS96 43A1 force field, as described: Pol-Fachin, L.; Fernandes, C.L.; Verli, H.: GROMOS96

[gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

2009-07-21 Thread Laercio Pol Fachin
Hi!   In a UBUNTU installation in dual boot (with Windows, in my case), GROMACS is approximatedely twice slower than in a installation in an entire HD.   If you need to install Linux in dual boot, maybe CentOS is a better choice.   Best regards, Laércio Pol-Fachin --- Em ter, 21/7/09, gmx-users-r

[gmx-users] Hydrogen Bond Lifetime

2008-09-30 Thread Laercio Pol Fachin
Hi, all. I am analyzing the hydrogen bond lifetime of water molecules around polar atoms of my molecule. However, I have faced different HB lifetime definitions in different sources. A sample of what I obtained employing g_hbond is below: "g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 1"

[gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

2008-12-08 Thread Laercio Pol Fachin
Dear GMX users: I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM. I have downloaded MOPAC7 for SourceForge, as linked in previous mails, and installed it. After, MPICH and fftw 3.0.1. So: "./configure --enable-mpi --with-qmmm-mopac" runs O.K., but, during "make": (some shell indi

Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

2008-12-09 Thread Laercio Pol Fachin
om: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=UTF-8; format=flowed Laercio Pol Fachin wrote: > Dear GMX

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

2008-12-11 Thread Laercio Pol Fachin
th files and objects (mopac7-1.10/src) or in LINUX folder with library files (usr/local/lib/)? Laércio Message: 2 Date: Thu, 11 Dec 2008 14:51:34 +0100 From: Gerrit Groenhof <[EMAIL PROTECTED]> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio

[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

2008-12-15 Thread Laercio Pol Fachin
dl There should be a -lmopac somewhere then. Try a make distclean, and reconfigure with the LIBS and LDFLAGS set. GErrit > > -- > > Message: 4 > Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST) > From: Laercio Pol Fachin > Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.

[gmx-users] g_sorient -ro output

2009-02-24 Thread Laercio Pol Fachin
Hi, all! I have a question about interpreting the output from a GROMACS tool, g_sorient. I'm analising the solvent orientation around some specific atoms of my molecules, using GROMACS 3.3.3. I have read the mailing lists, but I could not find anything specific about it (although the followin

[gmx-users] g_helix problem

2010-09-14 Thread Laercio Pol Fachin
Dear Gromacs Users: I have a problem when I try to run g_helix in Gromacs 4.0.5. I have two systems, each one containing a peptide, both with the same number of aminoacids; however, in one of them, most of the AA residues are not usual (in fact, they are post-translationally modified; thus, to