[gmx-users] Fwd: Known but still domain decomposition

Hi, Any help would be highly appreciated. Thanks. Alex -- Forwarded message -- From: Alex Date: Wed, May 2, 2018 at 5:32 AM Subject: Known but still domain decomposition To: gmx-us...@gromacs.org Deal all, I am doing coarse-grained bonded and nonbonded

Re: [gmx-users] index two groups for the distance calculation

Hi Mark, They have the correct number in the .gro file. Chain A has residues from 6 to 330 which contains my residue 159, chain B has residues from 1 to 30 which contains my residue 15. So if I select "r 15" when indexing there will be two residue 15 selected, one from chain A and one from chain

Re: [gmx-users] index two groups for the distance calculation

Hi, Look at the contents of the .gro file with the "less" tool and see what the numbering is :-) Mark On Wed, May 2, 2018 at 3:07 PM MD wrote: > Hi Gromacs, > > I was trying to index two amino acids to two groups and calculate the > distance between them. > > I used the

[gmx-users] index two groups for the distance calculation

Hi Gromacs, I was trying to index two amino acids to two groups and calculate the distance between them. I used the command "gmx make_ndx -f md.gro -o index.ndx" and tried to select residue 159 from chain A (group of r_159) and residue 15 from chain B. However, when I used the "l" function to

[gmx-users] gromacs with turbomole?

Hi, I am looking for viable systems for doing QM/MM calculations and as I have experience with both Turbomole and GROMACS I am wondering if there is anyone using these two together. I have found this ("The Quick and Dirty GROMACS-TURBOMOLE interface") at https://github.com/rmera/qdgt , but it

Re: [gmx-users] Inconsistent non-bonded energy when using energy tables.

Hi, Whether you will have a reasonable way to have your nonbonded interaction parameters combine with combination rules is up to you to decide, but AFAIK this should work. You will have a much better time trouble shooting your setup if you use

Re: [gmx-users] % of H-bond occupancy

Hi, Start by looking over http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-topic to see what is available. Mark On Wed, May 2, 2018 at 11:57 AM wrote: > Hii > I want to calculate % of H-bond occupancy between DNA base pair atoms and > Urea

[gmx-users] RDF calculation

Dear all, I have a curved rod-like micelle formed by three different molecules. I want to calculate the RDF of constituent molecules. I want to select the center line of the curved cylindir-like structure as a reference point. How can I do that? I am using Gromacs version 5.1.2. with Martini

Re: [gmx-users] Core dumped in NVT

Hi, That something is the output of another program does not necessarily make it a reasonable structure start MD. See http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#lincs-settle-shake-warnings. For example, some kind of void could exist that slams atoms around if

Re: [gmx-users] LJ-PME with user defined non-bonded parameters

Hi, Do check out the section on LJ-PME in the reference manual. The implementations are hard coded to the commonly used combination rules, thus arbitrary mixes of parameters are not supported. Mark On Wed, May 2, 2018 at 1:17 AM Lei wrote: > Hi, gmx users, > > I am

Re: [gmx-users] -ndec option of trjconv

Hi, See the release notes - http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html#removed-variable-precision-gro-writing Mark On Wed, May 2, 2018 at 3:45 AM Justin Lemkul wrote: > > > On 5/1/18 11:22 AM, Jicun Li wrote: > > Hi, > > > > Did anyone

[gmx-users] Inconsistent non-bonded energy when using energy tables.

Dear All, I will be working with a system having Lennard-Jones interactions between some species and Buckingham interactions between other species. I know this is possible using tables. As a first check to be sure I am doing the right thing, I set up a minimal system of two particles fixed in

[gmx-users] % of H-bond occupancy

Hii I want to calculate % of H-bond occupancy between DNA base pair atoms and Urea molecule in gromacs. Is it possible to do this in gromacs? If not then what is the way to do that? Thanks Sunipa  -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Known but still domain decomposition

Deal all, I am doing coarse-grained bonded and nonbonded parametrization using votca-gromacs. The "mpirun -np 64 gmx_mpi mdrun" work fine till step_021 of parametrization where it crashes because it can not find any domain decomposition for 64 ranks that is compatible with the system size. Even it

[gmx-users] Trans Dihedral Fraction

Dear Gromacs users, I tried to calculate fraction of trans dihedrals in my molecule using gmx angle -f traj.xtc -of -n dihedral.ndx -type dihedral However, I couldn't get dihfrac.xvg output file from -of option. What is the reason for this. Can anyone help me? Thank you. -- Gromacs Users