[gmx-users] (no subject)

Dear all, I have a protein_Ligand complex which I want  do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ). | | | GROMACS Tutorial | | | Here is my questiones:in tutorial he said:

Re: [gmx-users] non-water solvent + gmx solvate

Hi Kevin, Emailed to your address. Just to clarify, there is really only one issue, which is that we have a particular input that is making us stick with 2018. Once that's been figured out, I'll be able to enjoy the great new functionality in solvate. ;) Thanks, Alex On 5/27/2019 8:15

Re: [gmx-users] non-water solvent + gmx solvate

Hi Alex, Thanks for the followup, I've caught up on your previous thread with Szilard. Please do provide me the usage files for both issues at my uconn address. I'll certainly follow up on the gmx solvate stuff to make sure it works properly in the newest versions (since I did the most recent

Re: [gmx-users] non-water solvent + gmx solvate

Hi Kevin, I used insert-molecules for now to get acetonitrile where it needed to be, so it isn't much of an issue at the moment. We do have a more serious problem with upgrading to the latest version, and that is the 2019 mdrun either freezing or segfaulting on a particular simulation,

Re: [gmx-users] Question from new gromacs user

On 5/27/19 5:22 PM, Nabil Abid wrote: Dear i need to get some help concerning gromacs utilities and mainly how to get the full structure of protein (all system) from a generated extreme.pdb file (only c-alpha). thanks GROMACS has no ability to rebuild an entire structure. pdb2gmx can

Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file

On 5/26/19 9:13 AM, Lalehan Ozalp wrote: Thank you Justin, I worked more on the format of hydrogen names and I don't see those errors anymore. However, the only error I now see is: "Atom H5'1 not found in rtp database in residue FAD, it looks a bit like H01". Which is weird, because there is

Re: [gmx-users] Use of Restraint itps

On 5/22/19 10:54 PM, paul buscemi wrote: Justin, Certainly appreciate the help on this basic issue. getting closer…. I understand your response. Now, to clarify — how does the mdp ( or grompp ) know which itp file among the #include’s is to be used as the restraint file. Is that

Re: [gmx-users] Broken bonds between peptide and capped terminals when solvated

VMD has no knowledge of bonds, as all you fed it was a coordinate file. It makes guesses based on the separation of the atoms which atoms are bonded or not. So no bonds are being broken. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical

[gmx-users] Question from new gromacs user

Dear i need to get some help concerning gromacs utilities and mainly how to get the full structure of protein (all system) from a generated extreme.pdb file (only c-alpha). thanks Nabil Abid, PhD Assistant professor Bioinformatic,Molecular Biology, Virology  High Institute of

Re: [gmx-users] non-water solvent + gmx solvate

Hi Alex, I just looked back, and the 2018.3 release contained the fixes to gmx solvate that I was thinking of. If you're stuck on 2018 for other reasons, could you check to see if the problem persists in the most recent branch of that release family? I hope whatever other issue you're working

Re: [gmx-users] using GPU acceleration in gromacs

The log file output will show whether the device is supported. In general, all GPUs of compute capability >2.0 (codename "Fermi") are supported, and compute capability 2.0 devices were deprecated in the 2019 release (and are not supported in CUDA since mid 2017 either). -- Szilárd On Fri, May

Re: [gmx-users] Computational electrophysiology (compEL) setup issues

Dear Francesco, > On 27. May 2019, at 16:31, Francesco Petrizzelli > wrote: > > Dear gmx users, > > I'm trying to simulate change in the ion flux upon mutations using > Computational electrophysiology (compEL). > I have used packmol-memgen in order to generate the double bilayer using a >

[gmx-users] Computational electrophysiology (compEL) setup issues

Dear gmx users, I'm trying to simulate change in the ion flux upon mutations using Computational electrophysiology (compEL). I have used packmol-memgen in order to generate the double bilayer using a salt concentration of 1 M (3216 Cl- and 3168 K+). Then, I have setted up the simulation

[gmx-users] question regarding coulomb potential output

Dear all, I have a question regarding the output of the Coulombic energy from the edr file. I am looking at the interactions between two molecules, and trying to analyse the contribution of different interaction types between these two. Since hydrogen bonds are formed based on the charge

Re: [gmx-users] index file for special residues

Dear Dr. Dallas Warren Thanks a lot Maryam On 2019-05-27 02:09, Dallas Warren wrote: > "|" = or > > What you want is "&" = and > > aptamer | r special = aptamer > aptamer & r special = special > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash

Re: [gmx-users] GROMACS job opportunity: Scientific programmer at KTH Royal Institute of Technology (May 31 deadline)

Hi, This week's the last chance to apply for this job building some fun software with a great team and big impact! Mark On Fri, 3 May 2019 at 14:24, Mark Abraham wrote: > Hi GROMACS people, > > We are expanding the GROMACS team in Stockholm, so In case you are > interested in working on the