[gmx-users] MSD close to a surface/layer

Hi everyone, I have a simulation with a metal slab and I would like to get the MSD of the molecules close to the slab. I have tried the gmx selection that works pretty well to structural analysis, but to the dynamical analysis such as msd or rotacf there are some issues. I have tried the

[gmx-users] MSD close to a surface/slab

Hi everyone, I have a simulation with a metal slab and I would like to get the MSD of the molecules close to the slab. I have tried the gmx selection that works pretty well to structural analysis, but to the dynamical analysis such as msd or rotacf there are some issues. I have tried the

[gmx-users] RV: Running simulation differences

Hi Justin, Sorry for the misunderstanding. I am simulating the interaction of a lipid with water. I obtain practically the same value for the coulomb interaction energy, but I am not able to get a value for the van der waals energy close to the published one (although I have used the same

Re: [gmx-users] Running simulation differences

Hi Justin, Sorry for the misunderstanding. I am simulating the interaction of a lipid with water. I obtain practically the same value for the coulomb interaction energy, but I am not able to get a value for the van der waals energy close to the published one (although I have used the same

Re: [gmx-users] duplicated position restraint statements

That is way too much effort for not simply fixing the bug in the restraint generator, I hoped someone would just know off the top of their head ;) On Thu, Dec 20, 2018, 12:20 PM Justin Lemkul On Thu, Dec 20, 2018 at 2:08 PM Alex wrote: > > > Anyone? :) > > > > > Calculate a single-point energy

Re: [gmx-users] duplicated position restraint statements

On Thu, Dec 20, 2018 at 2:08 PM Alex wrote: > Anyone? :) > > Calculate a single-point energy on a given configuration with and without duplicates. If the energy differs, you have your answer. -Justin > > On 12/16/2018 2:54 AM, Alex wrote: > > Hi all, > > > > Quick question: in some of our

[gmx-users] Position restraints while performing pulling run for Umbrella sampling

Hi, I am intending to perform pulling run for umbrella sampling, on my coarse grained DNA protein system where I have a bundle containing 20 DNAs and proteins. I want to pull 1 DNA out of this bundle to perform Umbrella Sampling. I was going through this tutorial

Re: [gmx-users] duplicated position restraint statements

Anyone? :) On 12/16/2018 2:54 AM, Alex wrote: Hi all, Quick question: in some of our models, the list of position restraints as part of the permanent topology is created externally, based on the atomic positions. Unfortunately, there is a slight bug in the restraint generator and for a

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear Sir, > > Thanks a lot for the inputs. I tried incorporating the forcefield > parameters (directory) obtained from the atbserver in the working > directory. When i was trying to convert the

Re: [gmx-users] Running simulation differences

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi Justin, > > > Do you think that the difference between a value of -280 ± 37 kj/mol > obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable? > > As I said before, no, a

Re: [gmx-users] Running simulation differences

Hi Justin, Do you think that the difference between a value of -280 ± 37 kj/mol obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable? Thank you so much for all your help C. De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en nombre

Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

Dear Sir, Thanks a lot for the inputs. I tried incorporating the forcefield parameters (directory) obtained from the atbserver in the working directory. When i was trying to convert the protein.pdb to .gro, I noticed that the forcefield showed up in the menu as one included in local directory,