Re: [gmx-users] [~SOLVED] Problem compiling Gromacs 5.1 with XL

Hi Mark, I will send you the files. I managed to solve the issue by replacing the content of the ~/gromacs-5.1/src/gromacs/simd directory with files from Gromacs 5.0.6. Still curious about what could have caused such an issue. Best, Jernej Hi, That all seems wildly unlikely,

Re: [gmx-users] gromacs 4.6.1 installation problem

On 8/17/15 9:51 PM, Roshan Shrestha wrote: I am about to burst into tears now, since I am unable to get in touch with you guys. My problem is regarding the installation of gromacs 4.6.1, I followed exactly what was said in

Re: [gmx-users] gromacs 4.6.1 installation problem

Dear Roshan, Don't let it get to you! Gromacs is frustrating for all people relatively new. Sorry I can't help with your problem as I am not exactly an expert here but I am trying to provide moral support: hang in there! People are very helpful in the gromacs community and I am sure you will be

[gmx-users] gromacs 4.6.1 installation problem

I am about to burst into tears now, since I am unable to get in touch with you guys. My problem is regarding the installation of gromacs 4.6.1, I followed exactly what was said in https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-linux-users/ I followed with success till the

Re: [gmx-users] [~SOLVED] Problem compiling Gromacs 5.1 with XL

Hi, On Mon, Aug 17, 2015 at 11:23 AM Jernej Zidar jernej.zi...@gmail.com wrote: Hi Mark, I will send you the files. Unfortunately I can see no likely source of problems in them. A fresh build of 5.1 works fine for me. I managed to solve the issue by replacing the content of the

Re: [gmx-users] itp file - number of function

If you mean more than one term for a single dihedral, that would require function type 9 (see section 4.2.12 in the manual). Otherwise, if you specify a single dihedral more than once with different function type each time, I'm not sure what GROMACS would do. Hope this helps. Victor 2015-08-17

Re: [gmx-users] itp file - number of function

On 8/17/15 2:49 AM, Mehrnoosh Hazrati wrote: Dear all, hi in the case of writing the .itp file, is it correct to use different functions type for dihedrals?! Normally force fields don't mix different function types. If you're trying to hack together different parameter sets, this is

[gmx-users] box size and neighbor list cut-off

Dear Users, Hi. Box vector length: 3.448, 3.448, 3.448 nm dodecahedron. (Box volume is 28.98 nm^3) Diameter of tripeptide: 1.248 nm Volume of tripeptide: 0.35503 nm^3 (from genbox output) Short range Neighbor list cut-off: 1.1 nm (set manually by rlist=1.1)

Re: [gmx-users] Respect waters in crystallographic pdb file?

I haven't tried that before. May be you can open the .gro files before and after genbox with a text editor. Then, check those water molecules? Those water molecules might have the same residue id. On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all,

[gmx-users] Respect waters in crystallographic pdb file?

Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point

Re: [gmx-users] g_mmpbsa

On 8/16/15 12:38 PM, elham tazikeh wrote: Dear GMX Users is there anyone to help me in g_mmpbsa using for binding free energy calculation i have questions about *.mdp files as polar.mdp or for instance: what is the value of pdie in protein-ligand combinations i really appriciate for any

Re: [gmx-users] box size and neighbor list cut-off

On 8/17/15 2:02 PM, Johnny Lu wrote: Dear Users, Hi. Box vector length: 3.448, 3.448, 3.448 nm dodecahedron. (Box volume is 28.98 nm^3) Diameter of tripeptide: 1.248 nm Volume of tripeptide: 0.35503 nm^3 (from genbox output) Short range Neighbor list cut-off:

Re: [gmx-users] Respect waters in crystallographic pdb file?

On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote: Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box

Re: [gmx-users] box size and neighbor list cut-off

Sorry, I mean: If I use double precision gmx mdrun and constraint h-bonds, can I expect 1.135 rlist to give a drift in total energy as small as the one in the table? On Mon, Aug 17, 2015 at 5:07 PM, Johnny Lu johnny.lu...@gmail.com wrote: Thank you for the advices. I tried setting different

Re: [gmx-users] box size and neighbor list cut-off

Thank you for the advices. I tried setting different varlet buffer drift in the 1st equilibration run (nvt) for 5 seconds. From the log file of mdrun, I get: rlistverlet-buffer-drift 1.090.05 1.1140.005 1.1350.0005 = 1.1730.05 1.234

Re: [gmx-users] box size and neighbor list cut-off

Hi, Under the assumptions underlying the drift tolerance, yes. (It's actually slightly better than advertised, because of the use of discretized clusters.) At some point, the numerical perturbation from the constraint implementation dominates, as you can read about in the PDF reference manual and

[gmx-users] Problem compiling Gromacs 5.1 with XL Compiler

Hi, I am unable to compile Gromacs 5.1 using the XL compiler (version 12.1.0) on our BlueGene/Q cluster. Before starting I set the relevant paths like so: export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH export LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH export

[gmx-users] itp file - number of function

Dear all, hi in the case of writing the .itp file, is it correct to use different functions type for dihedrals?! Thanks you in advance Best Regards Mehrnoosh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Problem compiling Gromacs 5.1 with XL Compiler

Hi, That all seems wildly unlikely, particularly as you say you can compile earlier GROMACS versions with the same toolchain. The errors are caused by the compiler interpreting gmx_unused as a variable name, instead of a portable way to suppress compiler warnings about variables that are unused