[gmx-users] trjconv - two chains are separated

Hi Gromacs Users, I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories. My protein has two chains (A and B) and they closely bind to each other. after running trjconv with "-pbc nojump", two chains are greatly separated by a certain distance. It is mostly likely that the

Re: [gmx-users] AMBER nonbond params in GROMACS

Hi Mark, Thank you for your clear and thorough response! I can see how I completely missed that. Makes perfect sense now. :) Kind regards, Patrick On 2 February 2016 at 19:59, Mark Abraham wrote: > Hi, > > Thanks for the attention to detail! :-) > > On Tue, Feb 2,

Re: [gmx-users] trjconv - two chains are separated

For "-pbc nojump" to work, you need to make sure they are together (as you want) in the first frame of your input trajectory. The most reliable way to do this is by centering the trajectory on a residue at the interface between the two chains (using a custom index group). I've also heard some

[gmx-users] gromos43a1p-4.5.1.tgz can alos used for TPO and SEP

repected sir ! i also used the following forefield but it did not work. same error residue TPO is not found in residues topology database gromos43a1p-4.5.1.tgz Force field files for Gromos96 43a1p, re-formatted to be compatible with newer versions of Gromacs (4.0 and beyond). This particular

Re: [gmx-users] AMBER nonbond params in GROMACS

Hi, Thanks for the attention to detail! :-) On Tue, Feb 2, 2016 at 6:07 AM Patrick Charchar < patrick.charc...@rmit.edu.au> wrote: > Hello Gromacs Users, > > Sorry if this is trivial, but can someone please explain to me why LJ sigma > values in the gromacs implemented amber FFs

[gmx-users] atom name 1 in topol.top and conf.gro does not match

Dear Gromacs Users, I am trying to build topology file containing two different molecules (A molecule, and B molecule) "A" and "B" molecule contain three beads each. "A" molecules start from 1 to 600, and then "B" molecules start from 601 to 900 in conf.gro file. I created topol.top file

Re: [gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

Hi, Generally one would use acetyl or N-methylamine capping groups respectively for N and C termini of cleaved peptide bonds. These are often called ACE and NME in .rtp files. Mark On Tue, Feb 2, 2016 at 2:58 PM Dawid das wrote: > Dear Gromacs Experts, > > I would like

Re: [gmx-users] Nstlist and constrain simulations

On 02/02/16 14:04, Szilárd Páll wrote: > On Tue, Feb 2, 2016 at 11:17 AM, Michail Palaiokostas Avramidis > wrote: >> Hi Mark and thank you for your answer. >> Please see below :) >> >> On 01/02/16 18:28, Mark Abraham wrote: >>> Hi, >>> >>> On Mon, Feb 1, 2016 at 6:42

Re: [gmx-users] Verlet scheme and relative free binding energy

Hi, One can vary PME parameters for electrostatics at approximately constant accuracy by scaling the Fourier grid spacing and short-range cutoff by the same factor. (This is what mdrun does during PME tuning.) So you can use rcoulomb = 1.0 and spacing scaled accordingly. In GROMACS 2016, the

[gmx-users] Verlet scheme and relative free binding energy

Hi gmx-users, I have a question regarding the correct treatment of cut-offs for amber99sb-ildn in relative free binding energy calculations, using the verlet scheme. Many articles seem to use a 1.2 nm cutoff for coulomb interactions and a vdw interaction switched off between 0.9 and 1 nm (for

Re: [gmx-users] Nstlist and constrain simulations

Hi, On Tue, Feb 2, 2016 at 1:11 PM Michail Palaiokostas Avramidis < m.palaiokos...@qmul.ac.uk> wrote: > Hi Mark and thank you for your answer. > Please see below :) > > On 01/02/16 18:28, Mark Abraham wrote: > > Hi, > > > > On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis < > >

Re: [gmx-users] g_count

Hi, I don't know what g_count does, but there's a very general selection syntax implemented in gmx select, so e.g. you can express the geometric criterion there and count the size of the groups it finds. Mark On Mon, Feb 1, 2016 at 9:55 AM vgsplayer1 wrote: > > > Is there

Re: [gmx-users] Low GPU utilization

Hi, That sounds like it could just be normal for what you'd expect on a small-ish system if your GPU is better than your CPU. Sharing a .log file via a file-sharing service gives you a better chance of useful feedback. Mark On Mon, Feb 1, 2016 at 7:43 AM Hovakim Grabski

[gmx-users] Modified peptides

Hello I want to do protein-ligand MD with Gromos-43A1 ff. My ligand is a tripeptide with a heterocyclic ring attached to -N terminus. I read in Justin's tutorial, for non-peptidic ligands, one can obtain co-ordinates from PRODRG server. My question is, if i can obtain the co-ordinates for

[gmx-users] dna topology in OPLS force field

Hello, I am facing some difficulty to simulate single stranded DNA and a single walled acrbon nanotube. I need different CNTs (with various m and n) for my study and I am generating them using g_x2top accoring to Andrea Mineoi's tutorial. It seems to be ok. On the other hand I have to make

Re: [gmx-users] Nstlist and constrain simulations

Hi Mark and thank you for your answer. Please see below :) On 01/02/16 18:28, Mark Abraham wrote: > Hi, > > On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis < > m.palaiokos...@qmul.ac.uk> wrote: > >> Dear GMX users, >> >> >> I would like to ask about your opinion on the size of the

[gmx-users] US perl scripts gives empty

Dear all, im following tut for umbrella sampling for my structure i have pulled the ligand and visualized using pymol,when i run perl script i m getting some empty value for some configuration as below 4124.456 4134.480 4144.476 415 4164.524 4174.591 4184.498 4194.503

Re: [gmx-users] US perl scripts gives empty

On 2/2/16 8:35 AM, Nikhil Maroli wrote: Dear all, im following tut for umbrella sampling for my structure i have pulled the ligand and visualized using pymol,when i run perl script i m getting some empty value for some configuration as below 4124.456 4134.480 4144.476 415 416

[gmx-users] Rarefied trajectory

If need to generate for analysis a trajectory with fewer frames than in the original one (get 1000 frames from 10ns trajectory with 1 frames), what approach would be better: Use gmx trjconv with option '-skip 10', Or use gmx filter with options '-ol lowpass.xtc' and '-nf 10'? -- Gromacs

Re: [gmx-users] Rarefied trajectory

Hi Timofey, For further analysis you want trjconv. Filtering may yield nonphysical structures. Cheers, Tsjerk On Feb 3, 2016 7:22 AM, "Timofey Tyugashev" wrote: > If need to generate for analysis a trajectory with fewer frames than in > the original one (get 1000

Re: [gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

Hi, So does it mean that I need to change definition of each of my residues so that they do not contain the carbonyl C and O atoms for instance but instead the are bonded to the ACE "residue"? Best wishes, Dawid Grabarek 2016-02-02 16:17 GMT+01:00 Mark Abraham : > Hi,

[gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

Dear Gromacs Experts, I would like to perform MD simulation of a system consisting of few amino acids cut out of the protein. The thing is that I break some peptide bonds and I add methyl groups in this place. Now I am missing charmm22 parameters for proper bonds. Could you give me a tip on

Re: [gmx-users] Nstlist and constrain simulations

On Tue, Feb 2, 2016 at 11:17 AM, Michail Palaiokostas Avramidis wrote: > Hi Mark and thank you for your answer. > Please see below :) > > On 01/02/16 18:28, Mark Abraham wrote: >> Hi, >> >> On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis < >>