Re: [gmx-users] Centering the system

ts 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 > -- Andrew Gonchar Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

Re: [gmx-users] question

nd it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Andrew Gonchar Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://ww

Re: [gmx-users] question

macs.org/Support/Mailing_Lists > -- Andrew Gonchar Андрей Гончар -- 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

Re: [gmx-users] Continue simulation from the specific time

t; > > > > > On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар > wrote: > > > Hello, I've got a question. Is there a way to continue MD simulation, not > > from last state but from specific time of MD? Say we have made a MD, have > > analysed it and h

[gmx-users] Continue simulation from the specific time

frame, make all minimisations etc.? -- Andrew Gonchar Андрей Гончар -- 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

Re: [gmx-users] Mdrun_mip efficiency

or my questions, but I'm quite novice in running gromacs on cluster. 2013/5/21 Justin Lemkul > > > On 5/21/13 1:15 PM, Андрей Гончар wrote: > >> Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled >> mdrun with MPI. >> Now when I try

[gmx-users] Mdrun_mip efficiency

ss on cluster but I see the opposite. What I'm doing wrong? -- Andrew Gonchar Андрей Гончар -- 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

Re: [gmx-users] Fwd: Static compilation of gromacs

sers > * 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. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs

[gmx-users] Fwd: Static compilation of gromacs

statically linked instance of gromacs, copy it to another computer and use it from my home directory. -- Andrew Gonchar Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.o

[gmx-users] Extraction of low-energy conformations

Hello. How to extract all low-energy conformations from MD-trajectory of protein? -- Андрей Гончар -- 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

[gmx-users] Protein-ligand interactions in implicit water

Hello. Is it possible to perform MD for protein-ligand interactions in implicit water? And what about the precision of this kind of MD's? Are they differ strong from these with explicit water? -- Andrew Gontchar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

t to do molecular dynamics (MD) using gromacs of same ligand > and binding site of my protein. Thats why i want to know how to place ligand > in specific binding site and run MD using gromacs. > > Thanks, > Nitin > > > On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар wrote: &

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- 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 po

[gmx-users] Need help troubleshooting an mdrun-gpu error message!

Check the permissions on /dev/nvidia* I had OpenMM, CUDA driver and gromacs installed, but I was unable to run simulations on GPU until I've set permissions to 666 -- Andrey Gontchar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please se

Re: [gmx-users] Installing GMX-GPU 4.5.5

gt; make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 >>> make: *** [mdrun] Error 2 >>> >>> When I run make mdrun after deleting the 2 occurences of >>> "-fexcess-precision=fast" from CMakeCache.txt the compilation works. >>>

Re: [gmx-users] Installing GMX-GPU 4.5.5

x-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. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Su

Re: [gmx-users] Restraints for specific residues

Ok, thanks 2012/1/31 Mark Abraham : > On 31/01/2012 7:14 PM, Андрей Гончар wrote: >> >> So for every residue I need to specify their atoms, am I right? > > > Yeah. One way is to use make_ndx to select the atoms in the residues and > make an index file group, then

Re: [gmx-users] Restraints for specific residues

So for every residue I need to specify their atoms, am I right? 2012/1/31 Mark Abraham : > On 31/01/2012 7:06 PM, Андрей Гончар wrote: >> >> Hi! >> Is it possible to specify which residues to restrain during MD simulation? >> For example I have a protein, but I don

[gmx-users] Restraints for specific residues

Hi! Is it possible to specify which residues to restrain during MD simulation? For example I have a protein, but I don't want to restrain all the molecule, but a part. How can I do this? -- Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

anks in advance. > > > > Smitty > -- > gmx-users mailing list    gmx-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

Re: [gmx-users] Installation of gromacs-gpu on windows

I think so! 2011/7/8 Szilárd Páll : > I think you made the right decision! :) > -- > Szilárd > > > > On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote: >> Thanks a lot! >> Now we decided to use gromacs under linux and the installation of >> gromacs an

Re: [gmx-users] Installation of gromacs-gpu on windows

BRARY_PATh in cygwin). > > As I did this >1 year ago the above might not be accurate and slight > details might be missing. Let me know if you succeed. > > Cheers, > -- > Szilárd > > > > On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар wrote: >> Thank you

Re: [gmx-users] Installation of gromacs-gpu on windows

oth cmake and gcc > is available for cygwin so you might be lucky and get mdrun-gpu > compiled without any additional effort. > > All binaries on the Gromacs webpage _are outdated_ which is clearly > stated on the respective page. > > Cheers, > -- > Szilárd > > &g

[gmx-users] Installation of gromacs-gpu on windows

Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs unde