[gmx-users] compressibility values in coarse grained simulations

Dear all, I am using the coarse-grained molecular dynamics simulation to study membranes. In the production run .mdp file, to control the pressure I am using semiisotropic in the Pcoupltype option. I wanted to ask how many values I should give to compressibility and ref_p and what will happen if

Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?

*3 valence bond/. вт, 21 янв. 2020 г. в 10:19, Александр Лашков : > This ok. This term show non-bonded interaction for atoms > located through two valence bonds. > Alex > > вт, 21 янв. 2020 г. в 10:06, sunyeping : > >> Hi Justin, >> >> Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3

Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?

This ok. This term show non-bonded interaction for atoms located through two valence bonds. Alex вт, 21 янв. 2020 г. в 10:06, sunyeping : > Hi Justin, > > Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the > work. I still have a couple of questions: > > (1) When using the

Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?

Hi Justin, Thank you for reply. "energygrps = Protein LIG1 LIG2 LIG3 LIG4" can do the work. I still have a couple of questions: (1) When using the "gmx energy -f ie.edr -o ie.xvg" to extract the interaction energy, the interested energy terms should be input. Because there are four ligands

Re: [gmx-users] Making an index file for specific solvent molecules

On 1/20/20 11:31 AM, Aharon Gomez wrote: Hi everyone, I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules that are placed over some

[gmx-users] Making an index file for specific solvent molecules

Hi everyone, I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules that are placed over some distance to my protein. Is there any built in

Re: [gmx-users] RDF between larger molecules

On 1/20/20 10:00 AM, Gmx QA wrote: Thanks Justin! Can you also comment on the other issue, the lack of smoothness? I guess this is because I don't have that many individual coms per bin to accurately compute the rdf? At least I think that makes sense since when I increase the value of -bin in

Re: [gmx-users] RDF between larger molecules

Thanks Justin! Can you also comment on the other issue, the lack of smoothness? I guess this is because I don't have that many individual coms per bin to accurately compute the rdf? At least I think that makes sense since when I increase the value of -bin in gmx rdf I get an increase in

Re: [gmx-users] RDF between larger molecules

On 1/20/20 9:48 AM, Gmx QA wrote: Hi list, I am working on a system that contains lipids, but since there is no water present they do not form a typical bilayer. In these systems I also have some smaller drug-like molecules. What would be the best way to get a proper rdf-function between

[gmx-users] RDF between larger molecules

Hi list, I am working on a system that contains lipids, but since there is no water present they do not form a typical bilayer. In these systems I also have some smaller drug-like molecules. What would be the best way to get a proper rdf-function between the lipids and the drugs? Since both

[gmx-users] dssp version of gromacs 2019.3

Good day, I have downloaded the latest version of DSSP from the site : https://swift.cmbi.umcn.nl/gv/dssp/ however as I downloaded and extract the package I see it is named hssp 1.3.4 and the codes are different

Re: [gmx-users] Regarding high RMSD

On 1/17/20 11:01 PM, Ashma Khan wrote: Thank for your suggestion Alessandra I have applied the pbc conditions on my system in steps as follows: 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o

Re: [gmx-users] Protein pore collapse during simulation.

On 1/18/20 7:03 AM, Yogesh Sharma wrote: Hi I have used inflategro to pack protein in lipid bilayer. While simulation run protein channel is getting collapsed. can i get some suggestions, if it is because of the wrong orientation of my protein in bilayer or lesser area per lipid after

Re: [gmx-users] Selection/modifying tpr file

On 1/19/20 5:24 AM, Roshan Shrestha wrote: Dear all, I have a large system, but I want to extract only certain information from the tpr like make certain selection using index file. Is there any way I can extract certain information from the tpr file and save it as another tpr

Re: [gmx-users] how to include multiple energy groups for interaction energy calculation?

On 1/20/20 7:58 AM, sunyeping wrote: Dear all, I am doing MD simulations on a protein-ligand complex. This complex has 4 protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production

Re: [gmx-users] State of Matter

On 1/20/20 9:14 AM, Sina Omrani wrote: Thank you Christian, But my question is more about how to introduce state of the system. Does it depend on the temperature and pressure or force field parameters? Yes, all of them. There is no input parameter that says "this material is a

Re: [gmx-users] State of Matter

Thank you Christian, But my question is more about how to introduce state of the system. Does it depend on the temperature and pressure or force field parameters? On Mon, 20 Jan 2020 at 15:42, Christian Blau wrote: > Hi Sina, > > > You can have a look at order parameters of your system like

Re: [gmx-users] specific heat calculation using "gmx dos"

Hi Pragati, Answers in short: 1. It's only c_v, you'll have to add VT \alpha_T^2/ \kappa_T to obtain c_p 2. I suggest you use the approach in the paper, running an NVT simulation and base all on the c_v estimate. 3. To check convergence, I suggest running the analysis again on shorter parts

[gmx-users] how to include multiple energy groups for interaction energy calculation?

Dear all, I am doing MD simulations on a protein-ligand complex. This complex has 4 protein subunits, with each subunits binding one ligand, so there are 4 ligands (named LIG1, LIG2, LIG3 and LIG4, respectively) in it. I have finished the production run and get a trajectory, and now I want to

Re: [gmx-users] State of Matter

Hi Sina, You can have a look at order parameters of your system like angular distributions, orientations, local densities, etc. with analysis tools like gmx angle, h2order, order. Best, Christian On 2020-01-20 12:02, Sina Omrani wrote: Hi, I'm new to GROMACS and Molecular Dynamics and

[gmx-users] State of Matter

Hi, I'm new to GROMACS and Molecular Dynamics and I'm sorry if it is a witless question but how we can specify the state of a component (gas, liquid or super critical) in MD simulations? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Ran into trouble installing Gromacs API

Hi Marko, I'm sorry for the confusion. The install instructions for gmxapi 0.1 on GROMACS 2020 are at http://manual.gromacs.org/current/gmxapi/userguide/install.html I plan to update readthedocs in the next few days to cover both gmxapi 0.0.7 on GROMACS 2019 and gmxapi 0.1 (