Re: [gmx-users] unusual trajectory

Not an unusual structure at all. That is an issue with how VMD draws molecules, the bonds between them and a molecule appearing to be "broken" across the periodic boundary. VMD guesses where the bonds are, based on distances between the atoms, and they are formed when it first loads the molecule.

Re: [gmx-users] gmx distance

Take a look at http://manual.gromacs.org/documentation/2018.2/onlinehelp/selections.html to learn about the selection syntax in gromacs. There is an example in the examples section that does precisely what you want. "com of group 1 plus com of group 2" This can be used with gmx distance to compute

Re: [gmx-users] question

In reality, assuming your system is possible in reality, is there a magical being removing molecules to avoid "interference"? Alex On 7/23/2018 8:18 AM, Andrew Bostick wrote: Hi, I want to do md simulation of adsorbsion on small molecule on cnt and encapsulation small molecule into cnt. Shou

Re: [gmx-users] pdb2gmx: how to preserve original ions?

Thanks Justin and Mark! Following up by replying to a digest message (and switched to html formatting) so hope this looks nice... I decided to take Mark’s advice and convert to known restypes. Seems easy enough for ions since I haven’t started looking into what’s necessary for parameterization

Re: [gmx-users] gmx distance

Hi Andrew, I cannot answer your question about gmx distance but I have been using the MDAnalysis package for this kind of analysis. I am writing this in case you are proficient in python and need more flexibility. The code more or less would look like this: u=MDAnalysis.Universe(gro, xtc) g1 = u.

[gmx-users] gmx distance

Hi, I want to calculate distance between com of 2 groups (3 and 8) gmx_mpi distance -f md.xtc -s md.tpr -n index.ndx -oav dist.xvg After that: Available static index groups: Group 0 "System" (27599 atoms) Group 1 "Other" (716 atoms) Group 2 "MMM" (704 atoms) Group 3 "LIG" (12 atoms) Gr

[gmx-users] Nonbond params and pairtypes section in ffnonbonded.itp

Dear All, I've asked in my previous posts about how to supply parameters in the nonbond_params and pairtypes section of the ffnonbonded.itp, depending on different combination rules. From the manual, it seems that nonbonded parameters are calculated from the combination rules. >From the recent rep

[gmx-users] question

Hi, I want to do md simulation of adsorbsion on small molecule on cnt and encapsulation small molecule into cnt. Should I remove water molecules inside of cnt? Do these molecules interfere with the interaction between cnt and small molecule? Thanks AB -- Gromacs Users mailing list * Please sea

[gmx-users] Dihedral angles in crystaline structure

Hello, is anybody in this mailing list experienced in the parametrization of crystaline structures (i am working on metal organic frameworks) and is willing to answer some questions on dihedral angles? Kind regards Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centr

[gmx-users] Parameters for manganese Mn2+

Dear all, how can I convert AMBER parameters for usage in gromacs. In particular, I need parameters for manganese Mn2+. I found the corresponding AMBER parameters here: http://research.bmh.manchester.ac.uk/bryce/amber#ion Thank you very much! All the best Johannes -- _

Re: [gmx-users] make index

On 7/23/18 8:42 AM, farial tavakoli wrote: Dear GMX users I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command:   gmx make_ndx -f em.gro -o index.ndx Reading structure file Going to read 0 old index file(s) Analysing residue names:

[gmx-users] make index

Dear GMX users I am trying to make an index.ndx file of my complex which includes a receptor and a peptide using this command:   gmx make_ndx -f em.gro -o index.ndx Reading structure file Going to read 0 old index file(s) Analysing residue names: There are:   330    Protein residues There are:

Re: [gmx-users] gromacs 2018 for GPU install on cluster with truly static libraries?

Hi, Most of those are going to have the same problem and solution for every installed piece of software that uses CMake, so perhaps you already have some local knowledge to exploit or share? You can use -DCMAKE_EXE_LINKER_FLAGS="-static" and probably also -static-intel (see Intel's docs) in the f

[gmx-users] unusual trajectory

Dear Alex, Thanks for answer. "What I am trying to say is that per se nothing wrong seems to be happening" Based on your answer in previous post, can I use this trajectory for analysis? Best, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/M