[gmx-users] Question about COM-Pulling

into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax

[gmx-users] Question about COM-Pulling

is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email: mueck...@rhrk.uni

[gmx-users] Question about COM-Pulling

. I looked into older Gromacs manuals and in versions 4 it seems as if this data is printed to the pullx.xvg file or something similar. With kind regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0

[gmx-users] Question about COM-Pulling

Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no dummy particle as the spring extends between the reference group at z=1.1675 and the pull group, which in the first frame is located at z=1.1675

[gmx-users] Question about COM-Pulling

Dear Chris, thx a lot for your help! Unfortunately, the information you provided is nowhere to be found in the manual. With best wishes, Christian -- for your setup options, the spring potential is something like: U=0.5*k*[(z_ref

[gmx-users] Problem with coulombtype=user and 1,4 interactions

to reproduce densities etc. So what am I missing? Is it the potential that's wrong? Thanks alot for any ideas! Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email

[gmx-users] Role of epsilon_rf in implicit solvation

is this epsilon_rf also used in combination in implicit solvent models regarding the dielectric constant beyond cut-off? If yes, what would be an appropriate value for this constant? Best regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663

[gmx-users] Re: GB-polarization

Thanks for the clarification but I can't find anything in the .log or .edr-files that would correspond to the non-polar solvation energy. Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631

[gmx-users] Re: GB-polarization

that the ACE-type approximation is done by default (due to the manual) when using GBSA. Kind regards, Christian Christian Mücksch wrote: Thanks for the clarification but I can't find anything in the .log or .edr-files that would correspond to the non-polar solvation energy. I think you have

[gmx-users] GB-polarization

, -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Email: mueck...@rhrk.uni-kl.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] about sa_surface_tension

the simulation outcome. Kind regards, -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Email: mueck...@rhrk.uni-kl.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] About implicit water simulations

-field for instance or user-defined potentials with implicit solvent models? Best regards, Christian Mücksch -- Christian Mücksch Phone: +49 (0)631 205 4287 Department of Physics Fax: +49 (0)631 205 4965 TU Kaiserslautern Email: mueck...@rhrk.uni-kl.de Erwin

[gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

Dear all, so I downloaded Gromacs-4.5 and tried to compile the gpu-version with cmake version 2.8.0 as stated in the gpu installation instructions as export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5 make mdrun make install-mdrun But I

[gmx-users] Problems with GPU-Version and implicit water models

Dear all, I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only Amber-FF are working in the GPU-version. When I want to use the GBSA implicit water-model I have to use cut-off for the electrostatic interactions due to this error-message: ERROR 1 [file PR.mdp]: With GBSA,

[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

Dear All, I've been trying to compile and get Gromacs (version 4.0.7) working on a cluster that runs with Debian Lenny. I set the following variables: export SOFT=$HOME/GROMACS export PATH=$PATH:$SOFT/bin export LDFLAGS=-L$SOFT/lib export CPPFLAGS=-I$SOFT/include export