[gmx-users] MPI on single quad-core

mpirun -np" and "mdrun_mpi -nt" etc... Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] mdrun_mpi performance

t; etc and nothing seems to help... What is my problem??? Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

[gmx-users] Gromacs GMX_BUILD_FFTW warning in building Gromas 5.0.4

n would be extremely helpful!!! Thanks Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://mail

[gmx-users] Errors in building gromacs 5.0.4 MPI version

I got the following errors when I tried to install gromacs MPI version 5.0.4 on a Fedora 18 I wrote on the command line the following: cmake '/home/steve/Downloads/gromacs-5.0.4'-DGMX_BUILD_FFTW=ON -DGMX_MPI=ON  SCREEN PRINT OUT: -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so  --

[gmx-users] CMAKE compilation error

Thanks for your response. I have attached the files you asked forThe "Cmake_Screen.output" contains, at start, my cmake input command.... -Steve On 9/20/16 2:52 PM, Steve Seibold wrote: > Hello > I am attempting to compile Gromacs 5.0.4 mpi version and I get the state

[gmx-users] libfftw3f.so problems....

3f.so. The libfftw3f.so is a symbolic link to libfftw3f.so.3.2.4..Not sure what is going on In addition, I could not locate the GMXR executable for gmx?? Can someone help me with this??? Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] Installing/Uninstalling

? Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/lis

[gmx-users] OPLS problem

where in the screenprint outs or the gro files or system.top files… I also made sure that I was not getting a “cpp” error…. Does anyone know what the problem is here???  Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Umbrella sampling version 5.0

install 5.1.x but it failed...If necessary I will attempt to install 5.1.x, but only if it is necessary thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromac

[gmx-users] Distance Restraints

the grompp to make a tpr file.I have also place in "disre_fc = 1000" in my mdp file Can someone be explicit about what  I am doing wrong...I did get the "position restraint" to work, but am having trouble here. Thanks, Steve -- Gromacs Users mailing list

[gmx-users] Replica Exchange: Threads vs MPI

I apologize if this is a really crazy question; I just want to be sure that I understand everything. I am assuming after reading the Replica Exchange from the on-line gromacs site that you cannot run, perform this method with multiple threads on one one system. You must have several machines wi

[gmx-users] Water-Zinc interactions

I am doing a simulation of a protein with zinc ligands..When looking calculating the distance between the Zinc and the water, I am getting distances that go as low as 0.3-0.4 Angstroms. This seems too close to me..Is this close contact due to the errors in trajectories?? Thanks, Steve

[gmx-users] trjconv problems

it showed that this worked, but only for ONE zinc ligand ion...the other left the box with ligand to sulfur bond on 30-40 angstroms. Can someone tell me what is going on here...??? Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] Problems with trajectories

(positions) back onto initial structure which is in center of box. trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit progressive -o protein13A.trr This didn't help at all.. I am really at a loss here on how to deal with this and could use some help.. Steve --

[gmx-users] PBC problems??

or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up Thanks, Steve -- Gromacs Use

[gmx-users] Odd protein behavior in MD

procedure: trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc However, this did not correct the problem...Can someone please inform as to what the problem is??? The total energy and potential energy looks ok and so, I am lost as to what is happening or how to fix it. Thanks, Steve -- Gromacs

[gmx-users] Apple cluster

est in a small Linux cluster (~ 20-30 nodes) than to assemble this Apple cluster? Thanks, Steve -- View this message in context: http://gromacs.5086.x6.nabble.com/Apple-cluster-tp5014900.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list

Re: [gmx-users] problems with Cysteines

Thanks Justin I appreciate you help...Your comments made it clear... Steve -- View this message in context: http://gromacs.5086.x6.nabble.com/problems-with-Cysteines-tp5013859p5013870.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list

[gmx-users] problems with Cysteines

not allow any changes to Cys (to make s-s bonds or anything). Am I doing something wrong here? Could someone please tell me what I can do to make a S-S bond...do I have to use "specbond.dat"??? Thanks, Steve -- View this message in context: http://gromacs.5086.x6.nabble.com/pro

[gmx-users] Trouble with pdb2gmx and cysteines

Hello I am trying to make CYS in my topology file (and NOT CYSH or dissulfide bond). If my pdb file calls for Cys, I get CYSH .rtp type. I Then attempted to test the -ss command using pdb2gmx and this command is completely ignored. I don't get an error or any output suggesting its usage. I am us

Re: [gmx-users] editconf and "conect" option

older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks, Steve -- View this message in context: http://gromacs.5086.x6

[gmx-users] editconf and "conect" option

ine incorrectly. Here is what I have: $editconf -f name.pdb -o name2.pdb -conect I have a topology file in my working directory. I searched on line and in the forum, but can't find any info. Did I miss it? I would really appreciate any help. Thanks, Steve -- View this message in cont

Re: [gmx-users] Martini and Gromacs 3 and 4

"Unknown residue: %s\n"%resn ValueError: Unknown residue: ALA Therefore, I must have my "Mapping" directory in the wrong location?? I placed it in both the working directory and in /home/stevesei/bin but I keep getting the above message. I would appreciate any help..tha

[gmx-users] Martini and Gromacs 3 and 4

Martini FF? Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/ma