[gmx-users] GPU installation of gromacs:Tesla K20c

Dear all, i have Tesla K20 GPU and ubuntu 15.04 and i installed cuda 7.5.after that i executed the following commands tar xfz gromacs-5.0.5.tar.gz cd gromacs-5.0.5 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local

Re: [gmx-users] Dftb as qmmm method with gromacs

Hello Sir, I have modified the file CMakeCache.txt as suggested by you followed by make and sudo make install but while running mdrun I am getting the error: DFTB: SCC-DFTB mode 3! DFTB: PME will be done for QM/MM with QM atoms only, starting from 2nd SCC iteration (partial PME) QM/MM: MM e

Re: [gmx-users] Free Energy of Liquid Water

You were right, it's much faster when I only calculate free energy for one molecule. My simulation has 1000 water molecules in it, but I created a new topology file and gave one molecule a different name (but identical properties) and now it runs the same simulation in about 36% more time, which

[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

Dear all, I am joining a project where people are using the CHARMM22 force field. They converted a .prmtop file from Amber to Gromacs format with acpype. In the output topology, there are no Urey-Bradley potentials or improper dihedrals (for example, all the [ angle ] functions are of type 1 and n

Re: [gmx-users] Dftb as qmmm method with gromacs

Hi, Instead of the flag to Cmake you could also manually modify CMakeCache.txt //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess, // orca GMX_QMMM_PROGRAM:STRING=dftb best, Gerrit Message: 4 Date: Thu, 8 Oct 2015 09:51:38 +0530 From: Padmani Sandhu To: "gmx-us...@gromacs.org

Re: [gmx-users] pdb2gmx error

I definitely agree that it's odd that the warning only occurs with this specific residue. I ran a diff against the freshly downloaded AMBER03 files, but they were identical. I also tried running it again with freshly downloaded amber03 files in the directory. About the error: pdb2gmx never crashed

Re: [gmx-users] Differences between gmx bar and pymbar free energy

Hello again Scratch that, I had the input files numbered incorrectly for pymbar. Now all is well. Sorry for the confusion /PK 2015-10-08 13:22 GMT+02:00 Gmx QA : > Hi gmx-users > > I am running a series of free-energy of solvation calculations for small > molecules in water and octanol, to calc

Re: [gmx-users] pdb2gmx error

On 10/8/15 1:54 AM, Dries Van Rompaey wrote: Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not planning

[gmx-users] Differences between gmx bar and pymbar free energy

Hi gmx-users I am running a series of free-energy of solvation calculations for small molecules in water and octanol, to calculate partition coefficients. For this, I have set up a series of lambda-points in water and in octanol, and then haves used primarily gmx bar to evaluate the results. Usi

Re: [gmx-users] Virtual sites error

Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs. Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Labora

[gmx-users] NMA run problem

Dear Gromacs Users, I am trying to run a Normal Mode Analysis with Gromacs v5.0.4 of a structure of 18081 atoms (without water) and I have a problem. I did a several minimization of my structure (1 SD, 1 CD and 4 L-BFGS), and everything went well. You can see below the relative informations for

Re: [gmx-users] Testing mpi version of Gromacs 5.1

On Thu, Oct 8, 2015 at 11:56 AM, Joachim Hein wrote: > Hi everyone > > I hope this is the right place to discuss this. > > I am having issues with checking the correctness of my mpi version of > Gromacs 5.1. I have build and tested earlier versions without issues (e.g. > 5.0.4 is the latest I di

[gmx-users] Testing mpi version of Gromacs 5.1

Hi everyone I hope this is the right place to discuss this. I am having issues with checking the correctness of my mpi version of Gromacs 5.1. I have build and tested earlier versions without issues (e.g. 5.0.4 is the latest I did). I am also building float and double versions of the serial

Re: [gmx-users] PBC

I thought so :D Thanks! On Thu, Oct 8, 2015 at 9:37 AM, mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the > system is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during simula

Re: [gmx-users] A problem with potential energy values and openMP

Hi, This is normal. See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You will observe similar differences if you run with different numbers of MPI ranks. Mark On Thu, Oct 8, 2015 at 8:40 AM Milko Vesterinen < milko.j.vesteri...@student.jyu.fi> wrote: > Dear Gromacs users, >

Re: [gmx-users] PBC

Hi, On Thu, Oct 8, 2015 at 8:08 AM mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the system > is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during simulation. However in the

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, I can check all the possible combinations you listed in http://redmine.gromacs.org/issues/1834. Since my programming capability is limited, please direct me how to proceed for solving this issue? On Tue, Oct 6, 2015 at 9:00 PM, Teemu Murtola wrote: > Thanks for the clarification. I updated t