[gmx-users] Conversion of improper angles from amber object file to gromacs

  O    180    43.932    2 Are both entries required in the gromacs [ improper ] section or must I put only one of them? Thanks, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de -- Grom

[gmx-users] No compatible domain decomposition

the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't t

[gmx-users] Berendsen Barostat for production runs

s, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@bio.tu-darmstadt.de Don't trust atoms, they make up everything. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

ng now Tom Cheatham's > parameters (J. Phys. Chem. B, 2008, 112 (30), pp 9020–9041). > > I hope that helps > Best > Felipe > > On 08/05/18 15:54, Daniel Bauer wrote: >> Hello, >> >> >> We are trying to use amber99sb-ildn with gromacs2018.1 for simu

[gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

continuation = no lincs_order  = 4 lincs_iter   = 1 lincs-warnangle  = 30 morse    = no Best Regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cb

[gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

if the reduced bandwidth will hurt GROMACS performance due to bottlenecks in GPU/CPU communication and/or communication via InfiniBand. If this is the case, we might have to upgrade to new mainboards with dual x16 support. Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational

[gmx-users] Gromacs 2018 beta: g_membed broken?

   = 298.0    gen_seed    = -1   ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions comm-mode    = Linear comm-grps    = Other Water_and_ions Protein Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology &a

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

2/4/17 12:21 PM, Daniel Bauer wrote: >> Hello, >> >> I finally found my error in the conversion. As always, the devil is in >> the detail. I was under the assumption that parameters listed in the >> original forcefield files (toppar) are also sigma and epsilon values

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

). With the correct conversion term: eps = Rmin/(10*2^(1/6)) I can now reproduce the conversion of the numbers from the charmm implementation to gromacs (and thus know how to apply my NBFIX for this value). Thanks for your patience and best regards, Daniel On 12/03/2017 10:18 PM, Daniel Bauer wrote

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

are the way they are? It must be more than a direct conversion of the numbers from kcal to kJ. Or did I again made a mistake or took the wrong numbers? Best regards, Daniel On 12/03/2017 11:23 PM, Justin Lemkul wrote: > > > On 12/3/17 4:18 PM, Daniel Bauer wrote: >> Hello, >> &g

[gmx-users] Conversion of charmm36 parameters from namd to gromacs

not sure how to proceed without doing the reparametrization in gromacs again, because the stock values differ that much. Best regards, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt ba...@cbs.tu-darmstadt.de Don't trust a

Re: [gmx-users] Lipid Simulation Analysis

Hello, First of all you can try to reproduce basic lipid properties as the area per lipid and bilayer thickness. Both can be easily calculated from the position of lipid headgroups. Other useful properties is the diffusion rate of lipids (accessable by calculating the mean square displacement)

Re: [gmx-users] Continuation mdp flag

ption should be removed in favour of logic based around whether an > input checkpoint file (which can be constructed to be sane wrt the intended > simulation) was supplied to mdrun. > > Mark > > On Fri, May 5, 2017 at 3:54 PM Daniel Bauer <ba...@cbs.tu-darmstadt.de> &g

[gmx-users] Continuation mdp flag

Hello, This might be a trivial question for most of you but can someone give me more detail about what the 'continuation' flag in the .mdp settings does? The manual does not include a lot of information on that. Best regards, Daniel -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] CHARMM36 and energygroup exclusions

On 05/02/2017 07:45 PM, Justin Lemkul wrote: > > Your input configurations is probably broken across PBC, so grompp > does a clunky calculation and thinks things are split really far > apart. It doesn't matter though, because CHARMM36 doesn't use charge > groups. Every atom is its own group so

[gmx-users] CHARMM36 and energygroup exclusions

Hello, I need to run a simulation of a membrane system with CHARMM36 and energygrp exclusions. Therefore, I used the mdp settings suggested by the gromacs page but a lower rvdw-switch (0.8 instead of 1.0) to better reproduce DPPC lipid params: constraints = h-bonds cutoff-scheme = Group vdwtype

[gmx-users] CHARMM36 and energygroup exclusions

Hello, I need to run a simulation of a membrane system with CHARMM36 and energygrp exclusions. Therefore, I used the mdp settings suggested by the gromacs page but a lower rvdw-switch (0.8 instead of 1.0) to better reproduce DPPC lipid params: constraints = h-bonds cutoff-scheme = Group vdwtype

Re: [gmx-users] Exploding temp/pressure.

Did you forget to set an initial temperature distribution? In your mdp you set gen_vel to no. So it will not create an initial velocity distribution matching your temperature. For the first simulation of your workflow, you should set gen_vel: yes and continuation: no. Then for all simulation that

[gmx-users] Should I restrain omega dihedrals or just phi/psi?

also set restrains on omega dihedrals? (I dont think it matters but Im using Gromacs 2016.1) Best regards, Daniel Bauer -- 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 http