[gmx-users] bk3 water energy minimization potential shift

my coulombic cutoff? Would appreciate any input on these questions! Best, Jo ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.0005 nsteps = 100 ; For exact run continuation

[gmx-users] structure factor

Hi, Is there a way to calculate structure factor in gromacs? From the gmx rdf function? Thanks! -- 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

[gmx-users] tracking position of single particle

Hello, I would like to run a simulation where I need to track the position of a single molecule and determine the amount of time it moves a certain distance. Is there a way to do this in gromacs? Thanks! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] viscosity calculation using g_energy

10 ns and I saved energies every 1 ps but the >>>> results were far and the curves go to negative values. >>>> Please, do have an idea how to get accurate results? >>>> Thank you >>>> Ali >>>> >>>> >>> You give no infor

[gmx-users] viscosity calculation using g_energy

Hello, I would like to calculate bulk and shear viscosity on gromacs using g_energy. I have read a number of other emails about this topic but there still seems to be no conclusive answer to how to use this tool. I use the following command: gmx energy -f prod_500.edr -vis viscosity.xvg

Re: [gmx-users] gromacs 2018.1 installation

bra...@gmail.com> wrote: > Hi, > > Thanks - we need some more information to be able to help. What does > bin/gmx -version report? > > Mark > > On Wed, Mar 21, 2018, 19:28 Jo <jojo412...@gmail.com> wrote: > > > Hello, > > > > I have had s

[gmx-users] gromacs 2018.1 installation

' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:546: recipe for target 'check' failed make: *** [check] Error 2 Thanks, Jo -- 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

Re: [gmx-users] nve energy conservation

rom the paper <https://www.biorxiv.org/content/biorxiv/early/2016/10/24/083055.full.pdf>Mark referenced)? Thank you! On Tue, Mar 20, 2018 at 1:39 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Mon, Mar 19, 2018 at 10:08 PM Jo <jojo412...@gm

Re: [gmx-users] nve energy conservation

1000 On Mon, Mar 19, 2018 at 5:08 PM, Jo <jojo412...@gmail.com> wrote: > Hello, > > Thank you for your response. I have found a way to conserve energy of my > box of SPC/E water by removing 'settles' from my topology file. > Previously, the total energy of the system was co

Re: [gmx-users] nve energy conservation

about constraining the atoms as a rigid water molecule so that I don't loose energy conservation? Thank you in advance, Jo On Fri, Mar 16, 2018 at 4:51 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Fri, Mar 16, 2018 at 7:42 PM Jo <jojo412...@gmail.com> w

Re: [gmx-users] nve energy conservation

that 'settle' has not been a problem for energy conservation previously. I have also tried different versions of Gromacs (5.1.4 and 2018), but the energy shift still occurs. Can you recommend any other parameters to change? Or any other strategies to go about conserving energy for NVE? Best, Jo

[gmx-users] nve energy conservation

suggestions on what I can try or anything I am wrongly assuming! verlet-buffer-tolerance = -1 rlist = 1.3 coulombtype = PME rcoulomb = 1.3 coulomb-modifier = Potential-shift vdw-type = Cut-off rvdw = 1.3 vdw-modifier = Potential-shift Best, Jo -- Gromacs Users mailing list * Please search

[gmx-users] nve simulation

water, and I also suspect 'settles' could be causing the lack of energy conservation. Can anyone provide any suggestions on what I can do to conserve energy? I have attached the mdp file. Thank you, Jo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] viscosity calculation using Green-Kubo

Hello, I would like to calculate viscosity using the Green-Kubo method. I understand that the viscosity calculation using g_energy uses the msd method. Is there any built in command in gromacs for green-kubo? Or would I need to do that by hand? Thanks, Jo -- Gromacs Users mailing list

[gmx-users] viscosity calculation using g_energy

. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040458.html Can you please direct on what I might be doing wrong? Thank you, Jo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] couple-moltype

and Cl, defined as 2 molecule types). Is there a way that I can tell gromacs to include both molecules insertions in the free energy calculation? In the documentation, I could only find how to specify 1 molecule for the calculation. Thank you, Jo -- Gromacs Users mailing list * Please search