[gmx-users] correct rlist and Verlet scheme

I have trouble in correctly setting cut-offs with Verlet scheme to match force-field specific settings. It automatically adjusts cut-off and it looks like they change their values from ones recommended for the force field. Is there a way to correct it and set up them properly? The paper on FF

[gmx-users] F4-Order-parameter

Dear all, I am using GROMACS-4.6.5 for studying gas hydrates and related systems. A useful order parameter which indicates water to hydrate transition is the F4 order parameter where F4 is related to the H--O--O--H dihedral angle for a pair of water molecules Exact expression for F4 can be

Re: [gmx-users] correct rlist and Verlet scheme

There are people more qualified than me to explain the fine details of this, but in brief: Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if you rae using PME for the coulomb interactions), but by default it will adjust the neighbour list cut-off (rlist) to remain

[gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Dear all, I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q machine. This is using the xl compiler. I recieve the error: ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but the target platform supports only STATIC libraries. Building it STATIC instead.

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hi, Do the cmake versions differ? Mark On Fri, 12 Feb 2016 12:44 Hardy, Adam wrote: > Dear all, > > > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q > machine. This is using the xl compiler. > > > I recieve the error: > > > ADD_LIBRARY for library

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hi Mark, I was able to compile GROMACS on Marenostrum, the cmake version is "2.6-patch 2". On Fermi it failed, the cmake version is "2.8.8". This is not necassarily a fair comparison. I compiled using gnu on Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling compelled to

Re: [gmx-users] correct rlist and Verlet scheme

Hi, As Adam says, you want to understand the reason why the forcefield specifies the settings it does. For example, until at least AMBER 2003, their force field papers did not specify PME parameters more precisely than "x nm cutoff was used." If PME was used at all. ;-) So you can be guided also

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Sorry for the confusion, yes, find and replace Marenostrum with Juqeen for most of that last mail. Just got some PRACE test accounts and I got myself confused. The 2.6 version of cmake was from Marenostum before I’d loaded the proper module. Try again: Fermi (failed build, xl compiler) -

[gmx-users] PMF of a single water molecule respect to a surface

Dear Gromacs user, I am calculation the PMF of a single water molecule to pull it away from top of metallic surface along vacuum in the Z direction ,following the Justin umbrella tutorial. I am only interested in the behavior of PMF in 0.002 nm to 0.8 nm intervalon top of the surface, but I do

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hi, On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam wrote: > Hi Mark, > > I was able to compile GROMACS on Marenostrum, the cmake version is > "2.6-patch 2". > That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few versions now. On Fermi it failed, the cmake

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hello Adam For me alcf scientist suggested to compile with: Use xl compilers in your .soft environment. cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX

[gmx-users] Installation problem

Hi All, I'm trying to install GROMACS 5.1.2 on ubuntu 14.04 LTS. I used: cmake .. -DGMX_GPU=on -DGMX_USE_OPENCL=on -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON Everything went fine, but make ended with: [100%] Building C object

Re: [gmx-users] add parameter

Dear Justin, Thank you for your reply. I have parameters from some manuscript and add all of them in force field. There is two parts of dihedral types in ffbonded.itp that one of them has func=4 and another has func=9. Also I have two types of parameters for dihedral;* Proper* and* Improper

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hello Mark, This is the response I'm getting Please send your problem to gmx user forum http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List). Your problem seems come from Gromacs cmake command parsing. The related source code is pretty convoluted. Relevant Gromacs developer may answer

Re: [gmx-users] PMF of a single water molecule respect to a surface

On 2/12/16 8:47 AM, Alexander Alexander wrote: Dear Gromacs user, I am calculation the PMF of a single water molecule to pull it away from top of metallic surface along vacuum in the Z direction ,following the Justin umbrella tutorial. I am only interested in the behavior of PMF in 0.002 nm

[gmx-users] Prodrg disturbed hybridization state of doubly bonded nitrogen

Dear all,I am a beginner here. I have prepared my ligand topology file using prodrg, it gave me the following error, PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set 'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG> WARNING: deleted hydrogen(s) from your

Re: [gmx-users] Installation problem

Hi, What is your system details?Do you have GPU ,if yes CUDA library is installed? if not please install CUDA library and MPI packages too! hope it will fix -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] DSSP secondary structure

Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi, What command did you use to use their libxml2? Things work for me, but that doesn't mean there isn't a problem :-) Mark On Fri, 12 Feb 2016 20:41 Irina Kosheleva wrote: > Hello Mark, > This is the response I'm getting > Please send your problem to gmx user

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi, I have compiled my own libxlm2-2.9.3 (this is not a devel from what I know) Using: ./configure CC=mpixlcxx_r --prefix=/home/ikosh/programs/autotools-bin --with-python-install-dir=/home/ikosh/programs/autotools-bin --with -zlib=/soft/libraries/alcf/current/xl/ZLIB --enable-static