[gmx-users] Fixed Atoms minimization and MD

Dear GROMACS users, Is it possible to run a minimization (or MD) with some atoms fixed, in GROMACS? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe

[gmx-users] Gromacs 3.3.1 MPI/Itanium 2 fails to build

Hello, I have successfully built Gromacs 3.3.1 under Linux/Itanium 2 with the following configure options: ./configure -with-fft=fftw3 --without-x --prefix=$HOME/gmx331 When I enable MPI, the build fails: ./configure -with-fft=fftw3 --without-x --prefix=$HOME/gmx331 --enable-mpi;make snip ar

[gmx-users] failing to constraint distance

Dear Gromacs users, I have difficulties to get the distance between two molecules constraint using a .ppa file as described in Chapter 6 in the manual. I tried to combine the different options in almost all ways but nothing seems to constraint the distance. To check that the inter molecular

[gmx-users] Installing GROMACS 3.2.1 on SGI IRIX Origin

Hi Dr. David While searching, I saw the notes of Dr. Haruna from SGI: http://www.gromacs.org/pipermail/gmx-users/2005-August/016430.html I thought of installing gromacs-3.2.1 instead of 3.3.1 I have followed the procedure as given by Dr. Haruna and added 3 patches. It appears to

[gmx-users] Simulating a substrate

Hello everyone, I would like to simulate a carbon nanotube on a substrate. My idea is to make a 2D monolayer of closely spaced atoms that make an impenetrable wall. I will then restrain the positions of these atoms. I will then place the nanotube on top of it. However, I'm not quite sure what LJ

Re: [gmx-users] Installation Error on an Athlon64 with Intel Compiler

Hi again! Well, still having problems: /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_interactions.o mknb_interactions.c /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o

[gmx-users] Droplet vs. vesicle vs. big periodic box vs. implicit solvent

Hello, I would be grateful if anyone on the list could give me the benefit of their expertise on the following proposed simulation: System: 2 amorphous approximately spherical silica particles of diameter 2.5 nm, each with a net charge of -9e, with about 5 nm spacing between their centers

[gmx-users] tpr file

Hello all, Using trjcat I have joined 3 *.trr files and got final *.trr file. How to get/genetare corresponding *.tpr file ? According to manual, the tpr file extension stands for portable binary run input file. This file contains the starting structure of your simulation, the molecular

[gmx-users] Rgmax for single atom-water distributions

Dear Gromacs list members, Ineed obtain Rgmax parameters (with water H or O) and hydration energies for single atoms corresponding for example Amber atom types using mol dynamics. How can I introduce such single atoms in simulation with possibility to use specific for these atoms vdw

[gmx-users] ions in solvent

Hi! my system is DNA in a box with solvent. I want to put in the box a lot of ions (NA+, Cl-,). How can I do it? I want some of them dispersed in the solution, and some of them near the DNA molecule. thanks for your help. Beniamino Sciacca

[gmx-users] Problem in installing MPI version of Gromacs-3.3

Dear Gromacs Users, I have problem in installing MPI version of Gromacs-3.3 on linux cluster. I have installed fftw-3.0.1 in the Path /hpc/fftw3 and then have exported the include and lib path of fftw in my .bashrc file before installing gromacs-3.3. Now I want to install gromacs in the

[gmx-users] Problem in installing MPI version of Gromacs-3.3B

Dear Gromacs Users, I have problem in installing MPI version of Gromacs-3.3 on linux cluster. I have installed fftw-3.0.1 in the Path /hpc/fftw3 and then have exported the include and lib path of fftw in my .bashrc file before installing gromacs-3.3. Now I want to install gromacs in the

[gmx-users] How to view and analysis the result trajectory of g_covar?

Hi dear friends, I just get trajectory files using g_covar. But how can I view this .trr file? I tried VMD and gOpenmol, etc and do not work. Thanks. SJ Huang -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service.

Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program

Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to benchmark gromacs in A64s with different compilers. ;) Well, PGI

Re: [gmx-users] g_hbond lifetime output

Michael Torrice wrote: I am confused about the output from the hblife.xvg file of g_hbond. What exactly is the p(t) output? Is it the percent distribution of a given lifetime? If so, I have received p(t) data that sums up to anything from 0.1 toi 2. Check my recent paper: David van der

Re: [gmx-users] ions in solvent

Try:genion(genion -h)TsjerkOn 4/23/06, Beniamino Sciacca [EMAIL PROTECTED] wrote: Hi!my system is DNA in a box with solvent.I want to put in the box a lot of ions (NA+, Cl-,). How can I do it?I want some of them dispersed in the solution, and some of them near theDNA molecule.thanks for your

Re: [gmx-users] PGI compilation error: --rpath problem?

Jones de Andrade wrote: Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to benchmark gromacs in A64s with

Re: [gmx-users] Gromacs 3.3.1 MPI/Itanium 2 fails to build

[EMAIL PROTECTED] a écrit : Hello, I have successfully built Gromacs 3.3.1 under Linux/Itanium 2 with the following configure options: ./configure -with-fft=fftw3 --without-x --prefix=$HOME/gmx331 When I enable MPI, the build fails: ./configure -with-fft=fftw3 --without-x

Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program

hi, On Monday 24 April 2006 08:44, Jones de Andrade wrote: Hi all! Ok, I did not acquired to compile gromacs with intel yet, but now I'm also facing problems with PGI compilers (which also has the extra problem of needin to be redownloaded soon). Just in case someone asks: I'm trying to

Re: [gmx-users] Problem in installing MPI version of Gromacs-3.3B

Shankar Prasad Kanaujia wrote: Dear Gromacs Users, I have problem in installing MPI version of Gromacs-3.3 on linux cluster. I have installed fftw-3.0.1 in the Path /hpc/fftw3 and then have exported the include and lib path of fftw in my .bashrc file before installing gromacs-3.3. Now I

Re: [gmx-users] ions in solvent

Hi, Just add many ions randomly using genion. After equilibration, you'll find some of them in the solution and some near the DNA. Ran. Beniamino Sciacca wrote: Hi! my system is DNA in a box with solvent. I want to put in the box a lot of ions (NA+, Cl-,). How can I do it? I want some

Re: [gmx-users] Problem in installing MPI version of Gromacs-3.3B

Stéphane Teletchéa wrote: Shankar Prasad Kanaujia a écrit : Dear Gromacs Users, I have problem in installing MPI version of Gromacs-3.3 on linux cluster. I have installed fftw-3.0.1 in the Path /hpc/fftw3 and then have exported the include and lib path of fftw in my .bashrc file before

[gmx-users] Imaging in PBC simulations

Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a starting gro and than

Re: [gmx-users] Imaging in PBC simulations

I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.On 4/24/06, Martin LEPSIK [EMAIL PROTECTED] wrote:Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best wayto image a

Re: [gmx-users] Imaging in PBC simulations

Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a

Re: [gmx-users] Imaging in PBC simulations

Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a

Re: [gmx-users] LINCS deviation

Presumably this is with a standard, non-modified forcefield. One thing that might be worth trying (as, perhaps, a last resort) is reducing the timestep. It's a bad thing to have to do, because it reduces speed massively, but might help equilibrate your system and reduce whatever bad contacts are

[gmx-users] Re: PGI compilation error: --rpath problem?

Hi David. Well, I mentioned that change cause when compiling it with the PGI compiler the 3.3.1 version of gromacs yelded the exactly same error message: PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: ###) I just don't remember at this point the line number where

[gmx-users] Gromacs 3.3.1 MPI/Itanium 2 fails to build

Yes, I did make distclean before configuring with MPI enabled. Matt Ernst Washington State University [EMAIL PROTECTED] a écrit : Hello, I have successfully built Gromacs 3.3.1 under Linux/Itanium 2 with the following configure options: ./configure -with-fft=fftw3 --without-x

Re: [gmx-users] PGI compilation error: --rpath problem?

Hi all. Well, if I do not use the clue provided in http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html, I end up in the following error: . . . source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \ DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \ /bin/sh

Re: [gmx-users] Doubt in Distance Restraints

Hi Mr.Tsjerk, Thanks for your reply and I checked manual based on your suggestion. I just want to make it sure, Is it what the manual says while adding type 6 bond that is to edit the protein.top file under [bond] section so as to depict harmonic interaction