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

[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

[gmx-users] Discrepancy between RDF and Hbonds results

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

m atoms correspond to the cluster they form is not. > > > Dr. Vitaly Chaban > > > > > On Wed, May 1, 2013 at 2:40 PM, George Patargias > wrote: > >> Hello >> >> I am trying to calculate the MSD of 8 molecules in a lipid bilayer with >> g_msd. If

[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

you mean 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 > wrote: > >> Hello >> >> Doe anybody know what is the "best" (the

[gmx-users] ATP/Mg+2 parameters

meters for use 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 --

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

gt; INDIA > -- > 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_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. U

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

> On Tue, Mar 12, 2013 at 10:06 AM, George Patargias > wrote: >> Hi Carsten >> Thanks a lot for this tip. It worked! >> George >> > Hi, >> > On Mar 11, 2013, at 10:50 AM, George Patargias >> wrote: >> >> Hello >> >> Sorry for

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 wrote: > >> Hello >> >> Sorry for posting this again. >> >> I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration >&

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

single core so 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 li

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

out the Mac OS installers 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 wrote: >> Hi Szilαrd >> Thanks for your reply. I have run

[gmx-users] electron desnity

nce. 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/listinfo/gmx-users * Please search the archiv

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

lead to the CPU idling while waiting for the GPU. > > Cheers, > > -- > Szilαrd > > > On Thu, Feb 28, 2013 at 4:52 PM, George Patargias > wrote: > >> Hello >> >> We are trying to install the GPU version of GROMACS 4.6 on our own >> MacOS clus

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

/cuda-mac-driver.html Or is something else that we need to do? Many thanks in advance. George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

[gmx-users] Using AMBER FF with GROMACS

nde (2005), 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 B

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

[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