Re: [gmx-users] Free energy calculation of Histone

Hi, That's the wrong way around. :-) One doesn't do a lab experiment first and then decide what you wanted to observe from it, to either :-). There are tutorials for computing free energy of solvation, which I suggest you follow, and I suspect your fully solvated simulation won't be useful for

Re: [gmx-users] calculate interaction energy between two proteins

thank you so much. now i understand this. On 1/9/19, Justin Lemkul wrote: > > > On 1/9/19 3:31 AM, SHAHEE ISLAM wrote: >> it is connected with aggregation phenomenon. > > Maybe, but no force field is parametrized with protein aggregation in > mind. Mark is cautioning you that you may be seeking

[gmx-users] Free energy calculation of Histone

Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate

Re: [gmx-users] AMD 32 core TR

Tomas, Again, thanks for the response. On re-reading the data Exxact Corp sent ( always helps to review) they did use a 2080ti and two zions. Your point on maxing out the GPU is interesting. On the 8 core ( 16T) the GPU is maxed out as you inferred, but not on the 32 core (64T) with which

[gmx-users] free energy calculation for histone

Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate

Re: [gmx-users] Dihedral restraints

Thanks Mark for your reply In the log and edr files I only see an "Position Rest." term. So do you mean that the contributions on the dihedral restrains is added in in total energy without additional terms in the energy output in log file and the edr ? Thank you in advance for the

Re: [gmx-users] Status of GROMACS native Windows Builds

Hi, On Wed, Jan 9, 2019 at 4:54 PM Wahab Mirco < mirco.wa...@chemie.tu-freiberg.de> wrote: > There was currently a thread regarding ways of using Gromacs on > Windows systems. This cause me to try to download v.2019 to > a Windows build machine and see what the NATIVE BUILD looks like. > >

[gmx-users] Status of GROMACS native Windows Builds

There was currently a thread regarding ways of using Gromacs on Windows systems. This cause me to try to download v.2019 to a Windows build machine and see what the NATIVE BUILD looks like. Installed on the Machine and used for the build were: - Visual Studio 2017 ("Visual Studio 15 Win64" in

[gmx-users] gromacs 2016.3 solvate error for methanol water mixture

Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: ***

[gmx-users] Driver 410 solved the issue. Re: Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

Dear Paul and Mark, Thank you for the suggestions. I just upgraded NVIDIA driver from 384 to 410 and the problem is solved. Regards, Adarsh V. K. -- Message: 6 Date: Tue, 8 Jan 2019 18:29:18 -0600 From: paul buscemi To: "gmx-us...@gromacs.org" Subject: Re:

Re: [gmx-users] calculate interaction energy between two proteins

On 1/9/19 3:31 AM, SHAHEE ISLAM wrote: it is connected with aggregation phenomenon. Maybe, but no force field is parametrized with protein aggregation in mind. Mark is cautioning you that you may be seeking a meaningless quantity. To calculate the interaction energy, you need to define

Re: [gmx-users] RMSD plots protein-peptide complex

On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide

Re: [gmx-users] ramachandran plot

Hi Javed, I hope *gmx rama* will solve the issue. http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* DBT Research Associate, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New

Re: [gmx-users] Dihedral restraints

Hi, IIRC that's enough, for dihedral restraints. You will see energy contributions from the the restraints appear in your .log and .edr files if the restraints are active. I don't recall if there is anything printed by mdrun before the simulation commences. Mark On Wed, Jan 9, 2019 at 10:14 AM

[gmx-users] RMSD plots protein-peptide complex

Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. Thanks in anticipation --

Re: [gmx-users] ramachandran plot

Hi, I use the python MDAnalysis packages for this. https://github.com/MDAnalysis/mdanalysis/issues/1335 https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html Have a nice day, Tamas On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: Dear Users Can anyone suggest

[gmx-users] Help with gmx select

Hello, I want to use gmx select to get a list of protein residues that interact with PO4 beads (CG) in a bilayer: The command I am using is: gmx select -s system.gro -f traj.xtc -oi contacting_residues_DOPG.dat -resnr number -n PO4_index_1.ndx -select 'group Protein and same residue as

[gmx-users] RDF in gromacs

Hi, I am calculating the rdf of my system as follows. 1. rdf of oxygen atom of my drug and water this is successful (I just made an index file and for water i choose eg. 5 & a OW) this worked fine. 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the hydroxyl group of the

[gmx-users] ramachandran plot

Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain

[gmx-users] Dihedral restraints

Hello I would like to apply some dihedral restraints in different residues of my protein during the production stage. For that I have added at the end of the protein itp the section [ dihedral_restraints ]. Is it enough ? Should I add something else in the mdp ? In other words, how to be

Re: [gmx-users] failing of g_membed

Thank you for your replay. I will check it out On Wed, Jan 9, 2019 at 6:58 AM Mark Abraham wrote: > Hi, > > As I'm sure you know from reading up on membed, it works by scaling the > embedded protein to be tiny and turning off its interactions. The mostly > likely issue is that you didn't give

Re: [gmx-users] calculate interaction energy between two proteins

it is connected with aggregation phenomenon. On 1/9/19, Mark Abraham wrote: > Hi, > > How is the protein-protein interaction energy defined? What physical > observable is it connected to? > > Mark > > On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: > >> can anyone please tell me, if i select

Re: [gmx-users] calculate interaction energy between two proteins

Hi, How is the protein-protein interaction energy defined? What physical observable is it connected to? Mark On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: > can anyone please tell me, if i select 42 then wheather it will > calculate the protein-protein interaction energy? because i did