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• • Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 10 Justin Lemkul
• [gmx-users] MMGBSA for GROMACS Anwesh Pandey
  • Re: [gmx-users] MMGBSA for GROMACS Borkotoky Speaks
• [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites Rolly Ng
  • [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites Rolly Ng
  • Re: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites David van der Spoel
  • [gmx-users] 回复: Gromacs 2020 fails to run adh_cubic_vsites Rolly Ng
• [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2 Rana Ali
  • Re: [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2 Alessandra Villa
• [gmx-users] Can drude shell positions be minimized with keeping atoms positions restrained? Jones De Andrade
• [gmx-users] Minimize energy of protein in CCl4 Yang Li
• [gmx-users] mdp option periodic molecules Johannes Hermann
  • Re: [gmx-users] mdp option periodic molecules Christian Blau
  • Re: [gmx-users] mdp option periodic molecules Johannes Hermann
• [gmx-users] Regarding use of harmonic wall model Shashank Ranjan Srivastava
  • [gmx-users] Regarding use of harmonic wall model Shashank Ranjan Srivastava
  • Re: [gmx-users] Regarding use of harmonic wall model Justin Lemkul
  • Re: [gmx-users] Regarding use of harmonic wall model Shashank Ranjan Srivastava
  • Re: [gmx-users] Regarding use of harmonic wall model Justin Lemkul
  • Re: [gmx-users] Regarding use of harmonic wall model Shashank Ranjan Srivastava
• [gmx-users] 12 bead mapping of lipid Rabeta Yeasmin
  • Re: [gmx-users] 12 bead mapping of lipid Dave M
  • Re: [gmx-users] 12 bead mapping of lipid Rabeta Yeasmin
  • Re: [gmx-users] 12 bead mapping of lipid Sahil Lall
  • Re: [gmx-users] 12 bead mapping of lipid Rabeta Yeasmin
  • Re: [gmx-users] 12 bead mapping of lipid Sahil Lall
• [gmx-users] how to generate average structure from trajectory Sadaf Rani
  • Re: [gmx-users] how to generate average structure from trajectory Subhomoi Borkotoky
  • Re: [gmx-users] how to generate average structure from trajectory Sadaf Rani
  • Re: [gmx-users] how to generate average structure from trajectory Justin Lemkul
• [gmx-users] core dump Mohamed Abdelaal
  • Re: [gmx-users] core dump Dallas Warren
• [gmx-users] gmx hbond -life HaoLun Wu
• [gmx-users] how to add c-terminal to the coarse-grained structure Rabeta Yeasmin
• [gmx-users] Odd temperature spikes during T-REMD? Smith, Micholas D.
• [gmx-users] Bug or Feature? Energy Minimization + Restraints + Polarization Possible Issue? Jones De Andrade
• [gmx-users] Ellipticity 222 - negative values? Anh Mai
• [gmx-users] PEG from ATB: No residues in chain Schirra, Simone
  • Re: [gmx-users] PEG from ATB: No residues in chain Alessandra Villa
  • Re: [gmx-users] PEG from ATB: No residues in chain Schirra, Simone
  • Re: [gmx-users] PEG from ATB: No residues in chain soumadwip ghosh
• [gmx-users] Force field for urea and urea-TMAO mixture ISHRAT JAHAN
  • [gmx-users] Force field for urea and urea-TMAO mixture ISHRAT JAHAN
  • [gmx-users] Fwd: Force field for urea and urea-TMAO mixture ISHRAT JAHAN
  • Re: [gmx-users] Force field for urea and urea-TMAO mixture Alessandra Villa
  • Re: [gmx-users] Force field for urea and urea-TMAO mixture Erik Marklund
• [gmx-users] Regarding REMD using gromacs4.5.5 Amit Kumar
  • Re: [gmx-users] Regarding REMD using gromacs4.5.5 Daniel Burns
  • Re: [gmx-users] Regarding REMD using gromacs4.5.5 Amit Kumar
  • Re: [gmx-users] Regarding REMD using gromacs4.5.5 Mohammad Madani
• [gmx-users] GROMACS 2020.1 patch release available Paul bauer
• [gmx-users] Amber14SB Eduardo Mayo
  • Re: [gmx-users] Amber14SB Alessandra Villa
• [gmx-users] regard emails on unsubscription from the gromacs.org_gmx-users mailing list Alessandra Villa
• [gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs? Екатерина Одинцова
  • Re: [gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs? John Whittaker
• [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Justin Lemkul
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Justin Lemkul
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Paul bauer
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
  • Re: [gmx-users] GMX 2020 - COMM Removal Issue Daniel Kozuch
• [gmx-users] regarding dihedral restraints Sadaf Rani
  • [gmx-users] Fwd: regarding dihedral restraints Sadaf Rani
• [gmx-users] install and mdrun problems Bogdanov, Vladimir
  • Re: [gmx-users] install and mdrun problems Dallas Warren
  • Re: [gmx-users] install and mdrun problems Bogdanov, Vladimir
  • Re: [gmx-users] install and mdrun problems Kunal Dutta
  • Re: [gmx-users] install and mdrun problems Kamran Gul, M.Phil. Scholar, Institute of Chemical Sciences, UoP
  • Re: [gmx-users] install and mdrun problems Paul bauer
  • Re: [gmx-users] install and mdrun problems Bogdanov, Vladimir
  • Re: [gmx-users] install and mdrun problems Kunal Dutta
  • Re: [gmx-users] install and mdrun problems Timofey Tyugashev
• [gmx-users] PC turned off after starting minimization Bogdanov, Vladimir
• [gmx-users] grompp error : Atomtype CAro not found Atila Petrosian
  • Re: [gmx-users] grompp error : Atomtype CAro not found Dallas Warren
  • [gmx-users] grompp error : Atomtype CAro not found Atila Petrosian
  • Re: [gmx-users] grompp error : Atomtype CAro not found Justin Lemkul
  • Re: [gmx-users] grompp error : Atomtype CAro not found Dallas Warren
  • [gmx-users] grompp error : Atomtype CAro not found Atila Petrosian
  • Re: [gmx-users] grompp error : Atomtype CAro not found Justin Lemkul
• [gmx-users] Collision Mohamed Abdelaal
  • Re: [gmx-users] Collision Dallas Warren
• [gmx-users] How GROMACS can be compiled with subsystem Ubuntu 18.04 on Windows Server 2019 Standard? Kamil Rakowski
• [gmx-users] uni axial deformation with semi-isotropic pressure coupling at 1 bar Pragati Sharma
• [gmx-users] GROMACS 2019.6 patch release available Paul bauer
• [gmx-users] error on graphene sheet simulation Devargya Chakraborty
  • Re: [gmx-users] error on graphene sheet simulation John Whittaker
• [gmx-users] Z shell autocompletion Floris van Eerden
• [gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs Chenyu Liu
  • Re: [gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs Chenyu Liu
• [gmx-users] Restart energy minimization with step .pdb files Michele Pellegrino
  • Re: [gmx-users] Restart energy minimization with step .pdb files Quyen V. Vu
  • Re: [gmx-users] Restart energy minimization with step .pdb files Michele Pellegrino
  • Re: [gmx-users] Restart energy minimization with step .pdb files Justin Lemkul
  • Re: [gmx-users] Restart energy minimization with step .pdb files Michele Pellegrino
• [gmx-users] Error in ions.tpr generation Neha Tiwari
  • Re: [gmx-users] Error in ions.tpr generation Justin Lemkul
• [gmx-users] regarding calculation on shear viscosity shakuntala dhurua
• [gmx-users] Proximal RDF of water around protein? Rajeswari A.
• [gmx-users] regressiontests/complex (Failed) Navneet Kumar
  • [gmx-users] regressiontests/complex (Failed) Navneet Kumar
• [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy" Anh Mai
  • Re: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy" Justin Lemkul
• [gmx-users] Can GROMACS compute heat flux? James
• [gmx-users] Fwd: error during ions.tpr genereation. Neha Tiwari
  • Re: [gmx-users] Fwd: error during ions.tpr genereation. Justin Lemkul
• [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Andreas Baer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Paul bauer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Andreas Baer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Szilárd Páll
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Andreas Baer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Szilárd Páll
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Andreas Baer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Szilárd Páll
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Andreas Baer
  • Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Szilárd Páll
• [gmx-users] Umbrella sampling of peptide-membrane system Mijiddorj B
  • Re: [gmx-users] Umbrella sampling of peptide-membrane system John Whittaker
  • Re: [gmx-users] Umbrella sampling of peptide-membrane system Mijiddorj B
• [gmx-users] spliting of long trajectories to generate many small trajectories Priyanka Singh
  • Re: [gmx-users] spliting of long trajectories to generate many small trajectories Bratin Kumar Das
• [gmx-users] How to calculate the dihedral angle as a function of time? Sadaf Rani
  • Re: [gmx-users] How to calculate the dihedral angle as a function of time? Dallas Warren
• [gmx-users] replica exchange 1% Daniel Burns
• [gmx-users] Which output of gmx energy represents stress Pragati Sharma
  • [gmx-users] Fwd: Which output of gmx energy represents stress Pragati Sharma
• [gmx-users] Are parameters for NME group available for GROMOS 54a7? Carlo Martinotti
• [gmx-users] error occurred during simulation of HRAS protein (PDB ID: 3K8Y) in the presence of GTP, Calcium acetate, and crystal waters manindersingh rajawat
  • Re: [gmx-users] error occurred during simulation of HRAS protein (PDB ID: 3K8Y) in the presence of GTP, Calcium acetate, and crystal waters Dallas Warren
• [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory bonjour899
  • Re: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory Szilárd Páll
• [gmx-users] Automatically assign the protonation states for pdb2gmx ZHANG Cheng
  • Re: [gmx-users] Automatically assign the protonation states for pdb2gmx Mark Abraham
  • Re: [gmx-users] Automatically assign the protonation states for pdb2gmx ZHANG Cheng
  • Re: [gmx-users] Automatically assign the protonation states for pdb2gmx Mark Abraham
  • Re: [gmx-users] Automatically assign the protonation states for pdb2gmx ZHANG Cheng
• [gmx-users] Regarding gpu acceleration Faizan Abul Qais
• [gmx-users] How to avoid the infinite potential energy in simulations of dimers? Qing Liu
  • Re: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? Justin Lemkul
  • Re: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? Qing Liu
  • Re: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? Justin Lemkul
• [gmx-users] Thesis developed software; which Open-source License? Henry Wittler
  • Re: [gmx-users] Thesis developed software; which Open-source License? p.c.kroon
• Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul) Sadaf Rani
  • Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul) Justin Lemkul
• [gmx-users] restraints failure problem Sadaf Rani
  • [gmx-users] Fwd: restraints failure problem Sadaf Rani
• [gmx-users] couple-moltype in FREE ENERGY calculation hind ahmed
  • Re: [gmx-users] couple-moltype in FREE ENERGY calculation Justin Lemkul
• [gmx-users] PMF in inhomogeneous fluid phase Andreas Mecklenfeld
• [gmx-users] Output trajectory frames as separate coordinate files Peter Mawanga
  • Re: [gmx-users] Output trajectory frames as separate coordinate files Peter Mawanga
  • Re: [gmx-users] Output trajectory frames as separate coordinate files Justin Lemkul
• Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling? Groenhof, Gerrit
• [gmx-users] gmx trjconv -force option doesn't seem to work. 고연주
  • Re: [gmx-users] gmx trjconv -force option doesn't seem to work. Justin Lemkul
  • Re: [gmx-users] gmx trjconv -force option doesn't seem to work. Mark Abraham
• [gmx-users] cudaFuncGetAttributes failed: out of memory bonjour899
  • [gmx-users] cudaFuncGetAttributes failed: out of memory bonjour899
• [gmx-users] Converting Charmm to gmx format using cgenff Maryam
  • Re: [gmx-users] Converting Charmm to gmx format using cgenff Justin Lemkul
• [gmx-users] Selective RMSD calculation Peter Mawanga
  • Re: [gmx-users] Selective RMSD calculation Bratin Kumar Das
  • Re: [gmx-users] Selective RMSD calculation Peter Mawanga
  • Re: [gmx-users] Selective RMSD calculation Bratin Kumar Das
• Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) Sadaf Rani
  • Re: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) Justin Lemkul
• [gmx-users] MolVA 2020 Deadline Extension (February 29th) - EuroVis 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data Björn Sommer
• [gmx-users] Problem in energy minimization and domain decomposition Sadaf Rani
  • Re: [gmx-users] Problem in energy minimization and domain decomposition Justin Lemkul
• [gmx-users] Annealing Alex
• [gmx-users] Regarding to pme on gpu Jimmy Chen
  • [gmx-users] Regarding to pme on gpu Jimmy Chen
  • Re: [gmx-users] Regarding to pme on gpu Szilárd Páll
• [gmx-users] How to cap a single residue in gromacs Sadaf Rani
  • Re: [gmx-users] How to cap a single residue in gromacs Alessandra Villa
  • Re: [gmx-users] How to cap a single residue in gromacs Quyen V. Vu
  • [gmx-users] How to deal with unexpected reactions in umbrella sampling? Qing Lv
  • Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling? Quyen V. Vu
  • Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling? Qing Lv
• [gmx-users] GPU considerations for GROMACS hairul.ik...@gmail.com
  • Re: [gmx-users] GPU considerations for GROMACS Kevin Boyd
  • Re: [gmx-users] GPU considerations for GROMACS Jason Hogrefe
  • Re: [gmx-users] GPU considerations for GROMACS Szilárd Páll
• [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Robert Cordina
  • Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Alessandra Villa
  • Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Robert Cordina
  • Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Alessandra Villa
• [gmx-users] Listing residues in gromacs Subhomoi Borkotoky
  • Re: [gmx-users] Listing residues in gromacs Christian Blau
  • Re: [gmx-users] Listing residues in gromacs Subhomoi Borkotoky
  • [gmx-users] Listing residues in gromacs Subhomoi Borkotoky
• [gmx-users] Unexpected cudaStreamQuery failure: unspecified launch failure Mariem Ghoula
• [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation bonjour899
  • Re: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation Alessandra Villa
• [gmx-users] Is Gromos force fields not recommended? Myunggi Yi

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