[gmx-users] Fatal error: A coordinate in file box.gro does not contain a '.'

This error occurred while typing the following command: gmx solvate -cp box.gro -cs spc216.gro -o box_sol.gro -p topol.top basically what happened was that all the coordinates that were in my box.gro file were replaced by the word "-nan". I've never seen anything like this. can anyone tell why

[gmx-users] [ERROR] NI+2 in gromacs simulations

I inserted the following parameters in the aminoacids.rtp file: [ NI ] [ atoms ] NI opls_411 2.000 0 However, instead of the pdb2gmx command keeping the 2 atoms of NI + 2, two atoms of Nitrogen are added. Did I enter the parameters wrong? -- Gromacs Users mailing list * Please

Re: [gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67

gt;1. Gromacs 2019.3 compilation with GPU support (Prithwish Nandi) > 2. [HELP] Residue 'NI' not found in residue topology database > (Edjan Silva) >3. Re: Gromacs 2019.3 compilation with GPU support (Mark Abraham) >4. Re: [HELP] Residue 'NI' not found in residue

[gmx-users] [HELP] Residue 'NI' not found in residue topology database

Dear users, I am trying to perform a simulation with a protein which contains two nickel atoms in the active site. When using the pdb2gmx command the following error appears: 'NI' not found in residue topology database I have edited the ions.itp file in the force field directory used (opls)

[gmx-users] GROMOS force field for small molecules

Dear users, Is the use of the GROMOS force field for small molecules reliable? I performed complex DNA-LIG simulations and noticed slight distortions in the binding angles of some functional groups such as the −C ≡N

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 27

Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-

[gmx-users] HELP - Fatal error gmx pdb2gmx

I deleted all non-protein molecules and saved the file. I typed the following command: *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh* The error was as follows: *Fatal error:* *The residues in the chain MET1--PHE840 do not have a consistent type. The* *first residue has type 'Protein', while

[gmx-users] How to establish temperature variations during a simulation.

Dear users, I'm doing simulations with small molecules in implicit solvent. I'm using different temperatures. I wonder if it is possible to establish temperature variations during a single simulation. (For example: 100ns simulation where the temperature ranges from 220 K-330 k). Kind regards,

[gmx-users] Output files RMSD (xvg). Convert Nanometer to Angstrom.

Dear, There is some command to convert my output files from the molecular dynamics, so that I can visualize the deviation of the trajectories in Angstroms instead of nanometers. Respectfully. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Computational performance in version 2019-beta3.

Hello guys, I performed a 100 ns simulation using GROMACS: gmx mdrun, version 2019-beta3. The performance of my computer was 4ns / day. In previous versions, I performed similar simulations and obtained performace of 40 ns / day. I would like to know if something has changed in gmx mdrun's input

[gmx-users] How to calculate distance using gromacs?

Dear, I performed a 100 ns simulation with B-DNA. I want to know which gromacs option I can calculate the distance between two DNA residues (guanine 5 and ADENIN 6, for example) during the 100 ns of simulation. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Fatal error: Magic Number Error in XTC file

Dear, I was not successful running the following command: $ gmx rmsdist *-s* md_0_1.tpr -*f* md_0_1.xtc *-o *rmsdist.xvg GMX displays the following error: --- Program: gmx rmsdist, version 2019-beta3 Source file:

[gmx-users] Fatal error: Cannot find position restraint file restraint.gro

Dear users. I can not execute the following command: $ gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr The error message that appears is: - Program: gmx grompp, version 2019-beta3 Source

[gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?

I can not generate topologies for a medium molecule (beta-cyclodextrin) using the "gmx pdb2gmx". I've tested all the force fields. how to generate the topology files for beta-cyclodextrin using gmx? ---

Re: [gmx-users] Recovery simulation error (Bratin Kumar Das)

to the end of the command you typed add: -deffnm cbd211_md Em sáb, 17 de nov de 2018 às 08:00, escreveu: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >

[gmx-users] Best force Field for Protein

Dear Gromacs users, I will perform a simulation of a protein with explicit solvent to verify structural changes in temperatures of 300 k and 310 k. Given the various force fields available on the gromacs platform, which one would be most appropriate for my experiment? att. -- Gromacs Users

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.

ay's Topics: > >1. start the simulation of the last stopping point. (Edjan Silva) >2. Re: start the simulation of the last stopping point. (Paul Bauer) >3. Re: DispErsion correction (Farial Tavakoli) >4. Assigning charge to closely related functional group >

[gmx-users] start the simulation of the last stopping point.

Dear fellow scientists, I'm doing a 40ns simulation between DNA and a small molecule. It occurred that around 30 nanoseconds, the computer hung up. How do I start the simulation from the 30 nanoseconds performed? -- Gromacs Users mailing list * Please search the archive at