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
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
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"
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
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
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
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.
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
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
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