[gmx-users] standard error

Hi! What percent error is calculated as standard error by gmx analyze? 5%? Thank you in advance and regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/

[gmx-users] Protein-Ligand interactions

Hi Users. A basic clarification on protein and small molecule interaction. I have a docked complex of a protein-ligand (to accept, the docking score is too low). On simulation, even after applying position restraint, I find the ligand moving around the protein. Is this because there is any error

[gmx-users] calculation of pair wise interaction energy of residues

hi, Is it possible to calculate pair wise interaction energy of each residue. My protein consist of 129 residue. Because if i mention each residue as a group in mdp file then i will get a huge number of data. Which is very difficult to handle. Can anyone please suggest me how i can do this. Thankin

Re: [gmx-users] gmx grompp

That depends entirely on what is of interest from the simulation, and only you know those details. For most situations, as you noted, it isn't a concern, but you need to ensure that is actually the case. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Phar

Re: [gmx-users] gmx grompp

Thank you Justin. Yes, you are right as i noticed when tested the simulations with -t and without. However, i think it is not dangreous physically and the final results remain the same. Am i right? On Tue, Apr 16, 2019, 01:05 Justin Lemkul wrote: > > > On 4/15/19 8:36 AM, Amin Rouy wrote: > > Hi

Re: [gmx-users] -ignh command removes protonation site of interest

On 4/15/19 6:30 PM, Neena Susan Eappen wrote: Hello gromacs users, I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward? If you want another protonation state,

Re: [gmx-users] nstlist changes during equilibration and production

On 4/15/19 5:21 PM, Neena Susan Eappen wrote: Hello gromacs users, I set my nstlist to 10 steps for energy minimization, NVT equilibration and MD production run. However, for the latter two steps, nstlist changes from 10 to 100 (My time step for integration was set to 2 fs). Is 20 fs too fa

Re: [gmx-users] gmx grompp

On 4/15/19 8:36 AM, Amin Rouy wrote: Hi, Providing -t flag in grompp (gmx grompp -t nvt.cpt) is optional according to documentation. How does it influence on results? Checkpoint files are necessary for exact continuations. I'm asking because I have finished my simulation and only gave -c

[gmx-users] -ignh command removes protonation site of interest

Hello gromacs users, I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward? Many thanks, Neena -- Gromacs Users mailing list * Please search the archive at http://w

[gmx-users] nstlist changes during equilibration and production

Hello gromacs users, I set my nstlist to 10 steps for energy minimization, NVT equilibration and MD production run. However, for the latter two steps, nstlist changes from 10 to 100 (My time step for integration was set to 2 fs). Is 20 fs too fast to update neighbor list? Any impact on accuracy

[gmx-users] error particles communicated, 2/3 cutoff, domain composition - with a twist

Deaer Users, I've gotten the apparently common error "particles communicated to PME rank 19 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated." but with a twist. The 5 ns npt

[gmx-users] secondary structure analysis DSSP

Hello, I'm trying to evaluate the secondary structure of a monomer through the DSSP software. Combined with a Gromacs trajectory the output gives " Structure, Coil, B-Sheet, B-Bridge, Bend, Turn, A-Helix, 3-helix". This output is different from the standard DSSP program. I cannot find any document

[gmx-users] gmx grompp

Hi, Providing -t flag in grompp (gmx grompp -t nvt.cpt) is optional according to documentation. How does it influence on results? I'm asking because I have finished my simulation and only gave -c nvt.gro, not -t npt.cpt. Are my results correct? thanks for reply -- Gromacs Users mailing list *

[gmx-users] How to generate force field for carboxylated lysine residue?

Dear gromacs users Sorry for my previous email which has been sent by mistakenly. Coming to my problem, I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. T

[gmx-users] how to generate force field for carboxylated lysine?

Dear gromacs users I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. Then I got the topology file for carboxylated lysine ATB server. Now I have many questio