Tag: grompp

ERROR No such moleculetype NA – User discussions

GROMACS version:GROMACS modification: Yes/No I got this errorwhen I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10in the topol.top there is 3 NA atoms 🙂 GROMACS – gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C….

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Creating nacl in water system – User discussions

GROMACS version: 2018.6GROMACS modification: No I am very new to using gromacs, so I would appreciate any input.I am trying to set up a system of NaCl (JC) in water(spce) . I was able to run the tutorial simulation of lysozome in water. But in this the topology file was…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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Nvt.tpr -I couldn’t manage my nvt.tpr – User discussions

GROMACS version:2022-cp2k interface I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t. gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr nvt.mdb file :; md-nvt.mdp – used as input into grompp to generate nma-nvt.tprintegrator = md ; MD using leap-frog integratordt…

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molecular dynamics – How to generate a .tpr file from a .pdb or .xyz file in gromacs

For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp). Assuming, you are working with amber forcefield (a99ffSBdisp), Here’s how I do it. gmx pdb2gmx -ff a99SBdisp -f yourpdbfile.pdb -o water_1.gro -ignh -p topol.top gmx grompp -f water.mdp -c…

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[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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[gmx-users] grompp -check14

Post by Dongsheng ZhangDear all,Has anyone used -check14 for grompp? When I tried it just now, I gotsegmentation fault. grompp works fine without the option -check14 (orgrompp -f md01.mdp -c ala5 -p ala5 -check14 -o fullBack Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency…calling /lib/cpp…processing topology…Generated…

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[gmx-users] The grompp problem!! (Urgently)

I am doing the Drug-enzyme tutorial.I also generated the drg.itp, drg.gro files using PRODRG server.However, when I use the grompp command before the energy minimizationI face some error A fatal error was shown: atom types CR61 not found The atom type CR61 is presented in the drg.itp file that I…

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runing a command multiple times in different nodes in SLURM

I want to run three instances of GROMACS mdrun on three different nodes. I have three temperatures 200,220 and 240 K and I want to run 200 K simulation on node 1, 220 K simulation on node 2 and 240 K simulation on node 3. I need to do all…

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[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field.While running energy minimization I did get the error“No default Ryckaert-Bell. types”. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO)has No default Ryckaert-Bell. types. but on checking ffbonded.itp I foundthat this dihedral is…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Tau t gromacs manual

Tau t gromacs manual TAU at TACC – TACC User PortalBiomolecules | Free Full-Text | Electrostatics of Tau GN Drive Tau | The Gundam Wiki | Fandom Kirk took a break and sent out for coffee when a patrolman brought him…

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Queries regarding temperature gradient

Post by Sabreen FarnazDear all,This is in regard to my previous queries. The warning in NVT step canpossibly be ignored using -maxwarn but I am still not sure about the rest!Can someone please help? tau_t = -1 means temperature coupling is not applied. Whether that’swhat you want or not is…

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