[gmx-users] RDF of water

Do you have any suggestions about this? Should I run g_rdf in a different way? Thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users

Re: [gmx-users] RDF of water

Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF

[gmx-users] Discrepancy between RDF and Hbonds results

is this disagreement can be explained? Thanks Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] g_msd for many molecules

to the cluster they form is not. Dr. Vitaly Chaban On Wed, May 1, 2013 at 2:40 PM, George Patargias g...@bioacademy.gr wrote: Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index

[gmx-users] g_msd for many molecules

Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index file, will g_msd calculate the MSD of the center of mass of them or it will average over all atoms? Thanks George Dr. George

Re: [gmx-users] ATP/Mg+2 parameters

by best? It really depends on the force-field that you are using/intend to use. Best, Jo?o On Fri, Apr 26, 2013 at 4:00 PM, George Patargias g...@bioacademy.grwrote: Hello Doe anybody know what is the best (the most suitable) set of parameters to use for ATP/Mg+2 ? I have seen from

[gmx-users] ATP/Mg+2 parameters

with the AMBER force field. J Comput Chem 24:1016 I would appreciate if you can give me any hints on this. Thanks. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users

Re: [gmx-users] no CUDA-capable device is detected

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

-gpu_id 00 This is briefly explained on the wiki as well: http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multiple_MPI_ranks_per_GPU Let us know whether you are able to get useful speedup from GPUs! Cheers, -- Szil?rd On Tue, Mar 12, 2013 at 10:06 AM, George Patargias g

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

Hi Carsten Thanks a lot for this tip. It worked! George Hi, On Mar 11, 2013, at 10:50 AM, George Patargias g...@bioacademy.gr wrote: Hello Sorry for posting this again. I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration (CUDA 5.0 lib) using the following SGE batch

[gmx-users] Mismatching number of PP MPI processes and GPUs per node

that it matches the single GPU card. Do you have any idea what has to be done? Many thanks. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users

Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster

and releases, you'll have to do the research on that. Let us know if you have further (GROMACS-related) issues. Cheers, -- Szil?rd On Fri, Mar 1, 2013 at 2:48 PM, George Patargias g...@bioacademy.gr wrote: Hi Szilαrd Thanks for your reply. I have run the deviceQuery utility and what I got

[gmx-users] electron desnity

Hello In the g_density manual it is mentioned that When calculating electron densities, atomnames are used instead of types, this is bad So what should be included in the electrons.dat file. The unique atomtypes of the group or all the atomnames of this group? Thanks in advance. Dr. George

Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster

, -- Szilαrd On Thu, Feb 28, 2013 at 4:52 PM, George Patargias g...@bioacademy.grwrote: Hello We are trying to install the GPU version of GROMACS 4.6 on our own MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro 4000 cards: - We have downloaded and install the MAC OS X

[gmx-users] Using AMBER FF with GROMACS

), Biophysical Journal, 88, 2472-2493. The new GROMACS distributions have integrated the ffamber ports and there are quite a few papers where GROMACS is used in conjunction with AMBER FF. I just wanted to double-check. Many thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical

Re: [gmx-users] Removal of global rotation/translation

Many thanks for this Justin. On 1/31/13 11:53 AM, George Patargias wrote: Dear Gromacs list I would like to ask a question regarding the global rotation and translation removal in GROMACS. In my mdp file I use the following options: ; mode for center of mass motion removal comm-mode

[gmx-users] Removal of global rotation/translation

Dear Gromacs list I would like to ask a question regarding the global rotation and translation removal in GROMACS. In my mdp file I use the following options: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm