[gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

Dear Gromacs Users, Kindly consider this as my query mail as in the last mail, subject line was not complete. I apologize for the same . I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk water (TIP4P/2005 water) using reversible geminate recombination as mentioned in

[gmx-users] regarding

Dear Gromacs Users, I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk water (TIP4P/2005 water) using reversible geminate recombination as mentioned in Markovitch et al., J. Chem. Phys.,129,084505(2008). Following is the command which I have used : g_hbond -f NVT.xtc -s

Re: [gmx-users] Equilibration

That ultimately depends on what physical property you are hoping to show is at "equilibrium". For example, see https://twitter.com/dr_dbw/status/907735156382777344 for how temperature, total energy, volume, density and pressure change with time for an example system. Pressure and temperature you

[gmx-users] COM-pulling

Hello, I tried to do COM-pulling simulation (using Gromacs 5 .0.4) to pull a molecule away from sodium ion that is bound to acidic site of protein. My reference group is protein backbone. I do that in presence of solvent. The main problem is that my pulled group is not pulled in linear

[gmx-users] Equilibration

Dear users, I need to demonstrate that my box is in equilibrium. What is the maximum slope of the energy or the volume in function of time to demosntrate it? . Or exist anothe parameter to follow. Thank you very much. -- *Dr. Álvaro Ruiz * *Physicochemical Molecular LaboratoryDepartamento

[gmx-users] COM-RDF calculation

Hello, I am trying to calculate the center of mass (COM) rdfs for methanol molecules. I have noticed that in gromacs 2016 there is neither -com nor -rdf option for gmx rdf. I have used the following instead: gmx rdf -f traj.trr -n index.ndx -s topol.tpr -pbc -seltype whole_mol_com -selrpos

Re: [gmx-users] gromacs error

Hi, It's hard to say, but you should look at the log file and terminal output, and install the latest in the series of bug fixes... 5.0.7 rather than choose a version known to have dozens more bugs... Mark On Tue, Sep 12, 2017 at 3:55 PM Vidya R wrote: > Hi, > > I

Re: [gmx-users] gromacs error

Hi, I fixed that error. However,I now encounter a new one... GROMACS:gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit Groenhof

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello Wes, I ran some more test simulations. I think the error is because I added counterions to neutralize my system (it has a +2 charge) prior to the free energy. Without the counterions, the simulations are running fine. Though, I don't know whether such a behavior is expected. Such a setup

Re: [gmx-users] error sharing libraries...gromacs error

Hi, That command doesn't compile with the gcc compiler, does it? I already suggested what to do ;-) Mark On Tue, Sep 12, 2017 at 2:28 PM Vidya R wrote: > Hi, > > I now use > > export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin" > > But, how to fix that error? > > Thanks, >

Re: [gmx-users] error sharing libraries...gromacs error

Hi, I now use export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin" But, how to fix that error? Thanks, Vidya.R On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham wrote: > Hi, > > If you're trying to use the PGI compilers, then please don't because the > C++ performance is

Re: [gmx-users] error sharing libraries...gromacs error

Hi, If you're trying to use the PGI compilers, then please don't because the C++ performance is very poor. We recommend latest gcc or intel. Otherwise, configure GROMACS so that it uses the wrapper compilers when buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ etc.

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya wrote: > Just to add to the above post, running a none to vdw-q tranformation using > the following parameters also results in the same error for simulation at > first lambda. > Do you get this error on a normal

[gmx-users] error sharing libraries...gromacs error

Hi, I give these commands PATH=$PATH:"/usr/local/gromacs/bin/" export GMXLIB=/usr/local/gromacs/share/gromacs/top export LD_LIBRARY_PATH=/usr/lib export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" export

Re: [gmx-users] dielectric constant -reg

Hi, You haven't described what you're doing in enough detail for anybody to be able to suggest where you or the code might be doing something wrong. Mark On Tue, Sep 12, 2017 at 12:36 PM Meagha ramana kumar wrote: > hi mark, > > Same doubt in the following thread. > >

Re: [gmx-users] dielectric constant -reg

hi mark, Same doubt in the following thread. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html with epsilon_-surface =0, simulation runs fine. The problem starts when I give it a value. My model has only protein and doesn't have anything other than that. Moreover,

Re: [gmx-users] libgomp: Thread creation failed: Cannot allocate memory

Hi, Don't know, but likely something about your machine has changed since GROMACS was built, e.g. OS upgrade. I suggest you recompile. Mark On Tue, Sep 12, 2017 at 12:08 PM Neha Gupta wrote: > Hi, > > When I give this command > > gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm

[gmx-users] libgomp: Thread creation failed: Cannot allocate memory

Hi, When I give this command gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min I get this error libgomp: Thread creation failed: Cannot allocate memory What is the reason? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at