Re: [gmx-users] Problem with constant distance

Dear Justin, Thanks very much. Regards Samith On Wed, Dec 30, 2015 at 7:58 AM, Justin Lemkul wrote: > > > On 12/29/15 3:27 AM, Samith Rathnayake wrote: > >> Dear All, >> >> I just want to run a molecular dynamics simulation in gromacs with >> maintain a constant distance (like constrain t

Re: [gmx-users] Problem with constant distance

On 12/29/15 3:27 AM, Samith Rathnayake wrote: Dear All, I just want to run a molecular dynamics simulation in gromacs with maintain a constant distance (like constrain the distance) between two molecules in a specific period of time.(want to maintain the constant distance in the entire time

Re: [gmx-users] Umbrella Sampling and GPU

Yes On Tue, Dec 29, 2015 at 2:35 PM Nikhil Maroli wrote: > Dear users, > i would like to perform Umbrella sampling on few protein-ligand system, > i wanted to know is it possible to run it in GPU? (Tesla k20) > Thanks > -- > Ragards, > Nikhil Maroli > -- > Gromacs Users mailing list > > * Please

Re: [gmx-users] Can Gromacs 5.0~5.1.x perform Implicit solvent simulation

Hi, Implicit solvent support hasn't been actively maintained since GROMACS 4.5. If 4.5 running on a multi-core x86 is too slow, then you should explore other programs, e.g. AMBER Mark On Tue, Dec 29, 2015 at 2:01 PM Chunlei ZHANG wrote: > Dear Gromacs developers and other users, > > I would li

[gmx-users] Umbrella Sampling and GPU

Dear users, i would like to perform Umbrella sampling on few protein-ligand system, i wanted to know is it possible to run it in GPU? (Tesla k20) Thanks -- Ragards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

[gmx-users] Can Gromacs 5.0~5.1.x perform Implicit solvent simulation

Dear Gromacs developers and other users, I would like to simulate a protein complex of 0.5 million atoms by using implicit solvent model (i.e. GB model). I has successfully simulated the system with Gromacs 4.5.1 by using particle decomposition. But it is quite slow. Since versions > 5.0 support G

Re: [gmx-users] Calculate NMR shift from simulation

Hi, this task is quite challenging and up to now there are few valid protocols to quantitative correlate simulations with chemical shift calculations. Moreover you are dealing with chemical shift perturbation calculation, I mean the chemical shift variation due to either the dynamics of the syst

[gmx-users] Calculate NMR shift from simulation

Hi everyone , I have the shift in peak of amide proton and amide nitrogen of my protein in various polar organic solvent (40% solvent and rest water). I have simulated the protein in same condition. There is no major structural difference observed both by CD (ellipticity) and by simulation. The shi

[gmx-users] Problem with constant distance

Dear All, I just want to run a molecular dynamics simulation in gromacs with maintain a constant distance (like constrain the distance) between two molecules in a specific period of time.(want to maintain the constant distance in the entire time period). ​Is there any way to simulate this kind

Re: [gmx-users] Update Amber force fields, ff12SB abd ff14SB gromacs implementation testing

Hi, You can only get the total dihedral energy of all the dihedrals in your system. You can use e.g. gmx convert-tpr to make subsets of your .tpr for diagnosis, however. And you need to report some units on your energy differences ;-) Mark On Tue, Dec 29, 2015 at 6:41 PM Man Hoang Viet wrote: