[gmx-users] trans-membrane protein simulation

Hello gmx-users! I want to simulate a membrane protein, where it sets across the membrane (means that some of the protein's region lays outside the membrane and is water exposed). Obviously, the protein will be experiencing two different environments like membrane and water (heterogeneous

Re: [gmx-users] Generating topology file for a long polymer chain

Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including GMX_OPLS.itp , GMX_OPLS.top and

[gmx-users] Constraining starting configuration in Coarse-Grain Simulation

Hello, I am trying to run a CG simulation with only non-bonded interactions. I have obtained the tabulated potentials for those interactions by force-matching using VOTCA. I want all my bonds and angles to be constrained as they are in the initial cg_conf.gro file. Since I do not have tabulated

Re: [gmx-users] Gmx hbond

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin Thank you for your replyingBut you said in this tuturial, in order to have tc_groups = protein non-protein , it is

Re: [gmx-users] How to obtain a proper structure for glycine?

Oh, I'm sorry for misleading you. You need use -ter The -noter means that you DON'T want to choose protonation yourself. Give this one a try. 2017-08-06 20:38 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Dawid, > Thank you. However, I still got three hydrogens after running: > > > gmx

Re: [gmx-users] How to obtain a proper structure for glycine?

Hi Dawid, Thank you. However, I still got three hydrogens after running: gmx pdb2gmx -f gly_clean.pdb -o gly_processed.gro -water spce -noter gly_processed.gro: Glycine aRginine prOline Methionine Alanine Cystine Serine10 3936GLY N1 -0.191 -0.011 -0.008 3936GLY H12

Re: [gmx-users] How to obtain a proper structure for glycine?

Hi Cheng, By default, the termini of a polypeptide are charged. You need option -noter in your gmx pdb2gmx command to interactively tell it what charge (no charge in your case) you want for your termini. Best wishes, Dawid 2017-08-06 20:20 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Mark,

Re: [gmx-users] How to obtain a proper structure for glycine?

Hi Mark, Thank you. I have a glycine PDB: ATOM 1 N GLY 3936 -1.908 -0.113 -0.081 1.00 20.00 ATOM 2 CA GLY 3936 -0.753 0.774 0.097 1.00 20.00 ATOM 3 C GLY 3936 0.558 0.024 0.014 1.00 20.00 ATOM 4 O GLY 3936 0.474 -1.274

Re: [gmx-users] How to obtain a proper structure for glycine?

Hi, Prodrg is not gromacs software, so there is probably a better place to ask this question. I'd also look at their docs to find out how to suggest a carboxylic acid. Mark On Sun, 6 Aug 2017 18:09 ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I would like to perform simulations for

Re: [gmx-users] How to Identify clusters

Write a program that identifies contacts within a given radius...? > On Aug 6, 2017, at 08:53, Sameer Edirisinghe wrote: > > Dear all, > > I need to identify clusters in my polymer system. I have 200ns simulation > trajectory and using this how can I identify the clusters

[gmx-users] Non bonded interaction mapping

Dear all, I have done 200ns simulation for my polymeric system and I want to map all existing nonbonded interactions (i.e. H bonds) in my system over the time. Can anyone suggest me a method for this? Regards Bhagya karunarathna -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to Identify clusters

Dear all, I need to identify clusters in my polymer system. I have 200ns simulation trajectory and using this how can I identify the clusters existing in my system over the time? Need to find which molecules form the cluster. Can anyone suggest a method to do this? Regards Bhagya Karunarathna

Re: [gmx-users] TOPOLOGY USING OPLS FORCEFIELD

Hi, You need to insert ligand/small molecule information in top file, follow the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html -- Gromacs Users mailing list * Please search the archive at

[gmx-users] TOPOLOGY USING OPLS FORCEFIELD

Hi gromacs users, After getting the output from topolbuild, how to construct topology file using opls forcefield? Can anyone send useful links for the same? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at