[gmx-users] Implicit solvent for protein-DNA in GROMACS?

I'm looking for software able to perform MM for protein-substrate complexes. Currently I use in-house software working with implicit solvation. I'm interested in alternatives for this task. Are there any examples for such cases done in GROMACS? -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Maximum Force constant for Position Restraints

David, that's exactly right. For every timestep value, one can derive the appropriate upper limit for the restraint constant in a somewhat physically sound manner. I am just not entirely sure what was the purpose of the initial question, because for "infinite" restraint constant, I'd just freeze

Re: [gmx-users] Maximum Force constant for Position Restraints

On 2015-04-21 21:40, Alex wrote: No, it does not depend on the system content, aside from the mass of the particle. For a simulation requiring numerical integration in time, there is a limit, and I just estimated it above. For the real world, the limit is that there's no such thing as a harmonic

Re: [gmx-users] Tetrahydrofuran OPLS-AA forcefield

On 2015-04-21 20:07, André Farias de Moura wrote: Hi Marie, Topologies are much of a handcraft: I just read the description of atoms types within the OPLSAA GROMACS file and those types just seemed to match the chemical classification of the atoms comprising THF. You just need to check if atomic

[gmx-users] SWCN and graphene topology and coordinate

Dear gmx users,I saw some emailes regarding this in the mailing list but kinda confuesd so was wondering if anyone from the group can kindly provide me with the topology and coordinate files for SWCN and graphene?CheersMass -- Gromacs Users mailing list * Please search the archive at http://ww

Re: [gmx-users] Maximum Force constant for Position Restraints

No, it does not depend on the system content, aside from the mass of the particle. For a simulation requiring numerical integration in time, there is a limit, and I just estimated it above. For the real world, the limit is that there's no such thing as a harmonic position restraint. :) If you want

Re: [gmx-users] Maximum Force constant for Position Restraints

Thanks Alex. But then, theoretically, is there no limit? All depends on your system's content, right? 2015-04-21 16:16 GMT-03:00 Alex : > Correction: tau/pi on the left for the highest value and 5*tau/pi for the > 10 x period suggestion above. > > On Tue, Apr 21, 2015 at 1:13 PM, Alex wrote: > >

Re: [gmx-users] Maximum Force constant for Position Restraints

Correction: tau/pi on the left for the highest value and 5*tau/pi for the 10 x period suggestion above. On Tue, Apr 21, 2015 at 1:13 PM, Alex wrote: > I think this can be estimated from a general physical argument. The > absolute max in my opinion should come from > 4*pi*tau = sqrt(m/k), where m

Re: [gmx-users] Maximum Force constant for Position Restraints

I think this can be estimated from a general physical argument. The absolute max in my opinion should come from 4*pi*tau = sqrt(m/k), where m is the mass of the lightest restrained particle in the system, k is the constant you seek, and tau is the timestep. The coefficient is four because of the Ny

[gmx-users] Maximum Force constant for Position Restraints

Hi guys! Is there a maximum value of Force Constant for Position restraints? Reading the Manual I could only find the default and the equation to describe it. Best, -- Marcelo Depólo Polêto Group of Structural Bioinformatics - Center of Biotechnology Student of MSc Cell and Molecular Biology - U

Re: [gmx-users] Tetrahydrofuran OPLS-AA forcefield

Hi Marie, Topologies are much of a handcraft: I just read the description of atoms types within the OPLSAA GROMACS file and those types just seemed to match the chemical classification of the atoms comprising THF. You just need to check if atomic charges add up to zero, because otherwise you might

Re: [gmx-users] Extraction of the pdb data from the g_shame diagrams

and what the most trivial way to find correspondence of the line in the data file to what I actually see on the its graph (projection) ? Sorry I'm not an expert of xmgrace so it might seems for you trivial :) Regards, James 2015-04-17 20:18 GMT+02:00 Justin Lemkul : > > > On 4/17/15 11:52 AM, J

[gmx-users] Latest CHARMM36 + CGenFF 3.0.1 files

Hi All, We have updated our CHARMM36 force field files in concert with the new release of the CHARMM general force field (CGenFF). Please find the latest files on our website: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs Since the November 2014 release, the changes to the files i

[gmx-users] append does not work for me

Hi, I just tried to continue a simulation, after having extended the total time using gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 mdrun -nt 4 -deffnm xxx -cpi xxx.cpt xxx.cpt, xxx.log, and xxx.trr are present  in the working directory and are the original output files, i.e.,

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Dear Mahender: It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues/1346 ), though no reason is given. I'd

Re: [gmx-users] do_dssp for coarse-grained trajectory

Hi Tsjerk, Thank you for the reply. The coarse graining was done using MARTINI according to tutorials mentioned in their website. Best, Sandhyaa On Tuesday, 21 April 2015 12:46 PM, Tsjerk Wassenaar wrote: Hi Sandhyaa, DSSP doesn't work on C-alpha only or coarse-grained trajecto

Re: [gmx-users] do_dssp for coarse-grained trajectory

Hi Sandhyaa, DSSP doesn't work on C-alpha only or coarse-grained trajectories. Can you maybe specify what coarse-grain FF you're using? It may be possible to use the tool 'backward' to convert it to atomistic. Cheers, Tsjerk On Tue, Apr 21, 2015 at 6:48 AM, Sandhyaa Subramanian wrote: > Dear