[gmx-users] Stress/strain analysis

Dears, Can anyone explain to me if we can run a stress/strain analysis with Gromacs and if yes, how. Many thanks, Adama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_List

[gmx-users] Runs OK on small CPS but fails on large number of CPUs...

Dear Co-users, I have a systems made of simple molecules, KNO3 to say. A classical MD runs to completion on a supercomputer when using 24 CPUs only and fails after few hundreds of ps, not always at the same step, when I increase the number of CPUs to 72, 84, 96 ... "The error message is as follows

[gmx-users] Add new post-processing features in Gromacs

Dears, I would like to know if the details of how to add new post-processing features in Gromacs had been already discussed or described somewhere. I have in mind things like angle distribution, structure factor, and incoherent intermediate scattering function, to name a few, for glassy materials.

[gmx-users] How to add a new non-bonded interaction into Gromacs

Dear ALL: I would like to add a new 2-body non-bonded interaction into Gromacs. Has anybody done this yet? Help is dearly appreciated. Regards, Adama Adama Tandia, Corning INC, SP-TD-01-01 Corning NY 14831 USA, Tel: 607 248 1036 -GoogleVoice: 708 433 9430 -- gmx-users mailing listgmx-users

[gmx-users] Si-O-Si angle calculation with g_angle

Dear ALL: I have used GMX to study SiO2 in a glassy phase. Is it possible to use mk_angndx followed by g_angle to have the distribution of the Si-O-Si angles in the system? I have tried the following and end up with an empty ange.ndx file: mk_angndx -s silica.tpr -n angle.ndx -type angle

[gmx-users] Protocol describing how to add a new force field into Gromacs

Dear FOLKS, Is a standard protocol to add new force field into Gromacs developed/published somewhere? I have great interest in Embedded Atom Method, Modified EAM and Stillinger-Weber force field. These are force fields, I believe, that could help in a great deal the glass/ceramics community! Same

[gmx-users] Gro file with more than 99999 atoms

Dear ALL; I'm converting a file into a gro format but it has more than 9 atoms. How should I handle the first and fourth columns since I should keep them to five digits only? Thanks, Adama ___ gmx-users mailing listgmx-users@gromacs.org http://

[gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file

Dear ALL, I have generated from Accelrys (Materials Studio) a structure composed of a substrate topped by a layer of organic molecules. The structure can be saved into a .pdb format. Is there out there a tool that I could use to generate the corresponding topology file for Gromacs? Thank you in

[gmx-users] Conformation Search with Gromacs

Dear USERS, Can one use Gromacs for conformation search? If yes, how? Thanks, Adama _ Adama Tandia Modeling & Simulation Corning INC SP-TD-01-01 Corning, NY (USA) Tel: 607 248 1036 Fax: 607 974 3405 www.corning.com ___

[gmx-users] Genbox to generate box with isolated molecules...

Dears, I'm generating a box filled with NO3 molecules using Gromacs 3.3: genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0 -nmol 800 -vdwd 0.2 The file bigbox.gro is generated but molecules are entangled. This makes the geometry optimization to remove close contact impossib

[gmx-users] QMMM for element with "unknown" forcefield

Dear GMX users, I'm not very familiar with the QMMM implementation in Gromacs, but I have two questions. 1- I would like to run a MD simulation for glass materials that contain B and Sb based oxides. Both elements are known to be multivalent in the compositions that I'm interested. Is it

[gmx-users] Compile Gromacs-3.3.2 on HP xxxw9300 Workstation: AMD64 Opteron with Linux

Dear ALL; I'm trying to upgrade to GMX-3.3.2 with icc, ifort and mpich2. I used the following command with configure: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double --enable-fortran ""F77=ifort" "CC=icc" The compilation stops after couple of minutes and I get the followinfg erro

[gmx-users] Compilation error: eNR_NBKERNEL_NR

Hello ALL: Has anyone seen this error message before when installing GROMACS? nb_kernel_x86_64_sse2.c:98: error: `eNR_NBKERNEL_NR' undeclared here (not in a function) I used the following to compile Gromacs: ./configure --prefix=$HOME/GMX332 --enable-mpi --enable-double "F77=ifort" "CC=gcc" Need

[gmx-users] Accelrys to Gromacs

Dear users, Does anyone know a way to convert a typed structure from Discover Accelrys, using Compass or cvff, and export the structure into a topology and .gro files with all the force field parameters, LJ, bonds, angle, dihedrals ... I have seen this with Lammps (msi2lmp.exe) and I do not know i

[gmx-users] User specified Potential Functions

Dear all: I would like to use the User specified Potential Function to implement in Gromacs the modified force field from Winkler et al. [Journal of Chemical Physics, Vol. 120, No. 1, (2004) pp: 384-393] but I'm not sure I understand very well how this feature works in Gromacs for LJ type force fi

[gmx-users] Adding a new force field to Gromacs

Dear ALL: Is it documented somewhere how can one add a new non-bonded force field into Gromacs? I'm interested on adding the Stillinger-Weber force field, with two and three body contributions. Has anyone ever tried this before? Thanks in advance for your answers. Best wishes, Adama

[gmx-users] Relatively orient two molecules: rotation and/or translation

Dear Gromacs Users, I'm looking for an easy way to relatively orient two large molecules (many rings with long CnH2n+1 tails): keep one fixed and translate and/or rotate the second one with respect to a given direction. The idea behind would be to fill up then the box with a solvent and run a posi