Re: [gmx-users] Check the 1-4 interactions, and the non-bonded pairs in the output

Hi On Thu, Dec 5, 2019 at 7:01 PM Suvardhan Jonnalagadda < j.su.vard...@gmail.com> wrote: > Hi all, > > I have performed NPT simulation in GROMACS 5.4.1. In the 'forcefield.itp' > file I have mentioned 'gen-pairs' as 'yes', and also the 'Fudge-LJ' was > specified. From the output I want to check

[gmx-users] How to calculate potential energy with dynamics selection index?

Dear users, I am trying to calculate the VDW potential energy and electrostatic energy for solvent in the first solvation shell and in bulk for my simulation systems. In order to calculate the potential for solvent in the FSS, I have to do gmx_energy with dynamics selection and do a rerun.

Re: [gmx-users] The total charge is not integer : -0.00465

Dear Justin, Thank you for your answer. when I use just one chain of polymer with the protein, the charge is an integer but when I employ "insert molecules" to add more than one polymer chain, the charge will not be an integer. I am wondering what's the problem? Best regards On Tue, Dec 3, 2019

[gmx-users] Center of mass motion removal

Hi all, I have a droplet containing two molecules types of A and B in water. Unfortunately, I forgot to use the comm-grps = AB flag in my mdp file of simulations so, the whole droplet just drifting around inside water. Now at this point, I wonder if there is a tool in gromacs to remove the center

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Thanks for the quick response. I do have the environment properly prepare via modules. GW > On Dec 5, 2019, at 3:24 PM, Mark Abraham wrote: > > Hi, > > I suspect you need to prepare the intel environment at run time like you > did before compilation. Probably you (or a module you loaded)

Re: [gmx-users] Problem restarting job 2016.4 with gromacs 2019-4

Hi, A checkpoint restart is indeed not supported. But you can be creative with the old version of gromacs e.g. gmx grompp -f -p -c -cpi old.cpt -s new.tpr, and then that .tpr file has the content of the .cpt in a format that the newer gmx will be able to run (unless we actually removed necessary

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Hi, I suspect you need to prepare the intel environment at run time like you did before compilation. Probably you (or a module you loaded) source-d a compilervars.sh file, and that's probably what you need here. Mark On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh wrote: > > Also posted

[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Also posted on the intel forum: This problem is consistent with the following gromacs/compiler versions: Gromacs 2019.4/Intel Parallel Studio 2019.4 Gromacs 2019.4/Intel 2017.2 Gromacs 2018.2/Intel Parallel Studio 2019.4 Gromacs 2018.5/Intel Parallel Studio 2019.4 The command to build and

[gmx-users] Check the 1-4 interactions, and the non-bonded pairs in the output

Hi all, I have performed NPT simulation in GROMACS 5.4.1. In the 'forcefield.itp' file I have mentioned 'gen-pairs' as 'yes', and also the 'Fudge-LJ' was specified. From the output I want to check and confirm the LJ parameters of 1-4, and non-bonded pairs. How do I check it? Thank you, Best

Re: [gmx-users] run MD in vacuum

This settings work, but version isn't newest. integrator<>=<->md dt<><-->=<->0.001 nsteps<><-->=<->1010 nstxout><-->=<->1 nstcalcenergy<->=<->100 nstenergy<->=<->100 cutoff-scheme<->=<->group pbc<--->=<->no nstlist>=<->0

Re: [gmx-users] run MD in vacuum

On 12/5/19 8:59 AM, HERNANDEZ ALBA Oscar (ECPM) wrote: Hello Justin, I am starting using gromacs and I am still discovering all the different possibilities that this software offers. However, I want to run MD in vacuum, not in solution. I read that the newest versions

[gmx-users] run MD in vacuum

Hello Justin, I am starting using gromacs and I am still discovering all the different possibilities that this software offers. However, I want to run MD in vacuum, not in solution. I read that the newest versions of gromacs (from 2019) allows to perform molecular dynamics in

Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

Can you please file an issue on redmine.gromacs.org and attach the inputs that reproduce the behavior described? -- Szilárd On Wed, Dec 4, 2019, 21:35 Chenou Zhang wrote: > We did test that. > Our cluster has total 11 GPU nodes and I ran 20 tests over all of them. 7 > out of the 20 tests did

Re: [gmx-users] Potential or total energy in dhdl files

Hi, On Wed, Dec 4, 2019 at 11:39 AM Александр Лашков wrote: > Thank you for anwer, but i don't understand this. For BAR this terms not > necessary. But for MBAR i'am not sure. In third party program - alchemlyb > and alchemystry-analysis, total energy or potential used for calculate > reduced

Re: [gmx-users] Help installing do_x3dna

Hi Salvador, If you did not have any luck so far, trying to contact the author of the tool, Rajendra Kumar, directly might help: https://scholar.google.com/citations?user=zYKuBCcJ=en Best, Christian On 2019-11-21 21:00, Salvador Herrera-Velarde wrote: Dear All, I am trying to install

Re: [gmx-users] How to calculate the spatial distribution function for the last 50ns of the trajectory?

Hi Peiyin, There is a related redmine entry that suggests this might be fixed in newer versions of GROMACS https://redmine.gromacs.org/issues/2189 (from GROMACS2018 on). If you are using a newer GROMACS version, to rule out that this is an issue related to .tng, can you try using the older