[gmx-users] please, how edr data is xdr packed?

Hi there, I am trying to use python xdrlib module to read edr files but not knowing how the data is packed using the xdr protocol makes my work very difficult, if not impossible. Would someone kindly tell me how data is packed in the edr file? Or where it is the gromacs code so I can try to figur

Re: [gmx-users] please, how edr data is xdr packed?

On 2010-08-22 13.14, Alan Wilter Sousa da Silva wrote: Hi there, I am trying to use python xdrlib module to read edr files but not knowing how the data is packed using the xdr protocol makes my work very difficult, if not impossible. src/gmxlib/enxio.c Would someone kindly tell me how data is

[gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

I'm looking for an rtp file for charmm in gromacs and according to http://www.gromacs.org/Downloads/User_contributions/Other_softwareIt should be available in a file called charmm_gromacs.tar.gz athttp://www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz but the link is

Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

On 2010-08-22 15.16, Michael McGovern wrote: I'm looking for an rtp file for charmm in gromacs and according to http://www.gromacs.org/Downloads/User_contributions/Other_software It should be available in a file called charmm_gromacs.tar.gz at http://www.gromacs.org/old/topologies/uploaded_force_

[gmx-users] Metallic boundary conditions

Hi, I want to use metallic boundary conditions in my problem. I think one can do that with the option epsilon_r =0 in gromacs. If I set epsilon_r =0 I get the output: Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Dipoles' 1000 steps, 5000.0 ps. Segmentation fau

Re: [gmx-users] Metallic boundary conditions

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 08/22/2010 05:29 PM, poj...@icp.uni-stuttgart.de wrote: > Hi, > > I want to use metallic boundary conditions in my problem. > I think one can do that with the option epsilon_r =0 in gromacs. > If I set epsilon_r =0 I get the output: > Metallic

[gmx-users] Metallic boundary conditions

Hi, thank you for your answer. What is then epsilon_r ? regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the lis

[gmx-users] Charmm to Gromacs: Polyols force field

Olá pessoal, Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009, 5, 1315). I am very interested in using it in GROMACS. For this, I began the transfer of the parameters with the following recipe: 1) All atom types were added to the atomtypes.atp file; 2) All bonded parame

Re: [gmx-users] Charmm to Gromacs: Polyols force field

Eudes Fileti wrote: Olá pessoal, Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009, 5, 1315). I am very interested in using it in GROMACS. For this, I began the transfer of the parameters with the following recipe: 1) All atom types were added to the atomtypes.atp

[gmx-users] PMF

Hi, All I am trying to calculate pmf for enzyme ligand complex using the tutorial of umbrella sampling. I have successfully created the unit cell around the protein and have solvated. The ions were also added by genion. But when I run the minimization step with the command grompp -f minim.mdp -