December 2014 Archives by thread
Starting: Mon Dec 1 07:19:06 CET 2014
Ending: Wed Dec 31 21:08:30 CET 2014
Messages: 624
- [gmx-users] Can we calculate rmsd from after energy minimization?
Seera Suryanarayana
- [gmx-users] error in PME mesh load
RINU KHATTRI
- [gmx-users] Free Energy calculations crash for lambdas higher than 0.8
Julian
- [gmx-users] odd replica excahnge
leila salimi
- [gmx-users] charmm to gromacs
Rebeca García Fandiño
- [gmx-users] Define Heavy Water
xy21hb
- [gmx-users] g_angle
ayşe K
- [gmx-users] Отв: Position Restraint or remove COM from DNA
Justin Lemkul
- [gmx-users] Why the rmsd value has been varied from different hardware for same protein?
Seera Suryanarayana
- [gmx-users] Continuing inturepted REMD simulation
Nizar Masbukhin
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 1
Seera Suryanarayana
- [gmx-users] charmm to gromacs
Jernej Zidar
- [gmx-users] read trr file
Tsjerk Wassenaar
- [gmx-users] read trr file
Tsjerk Wassenaar
- [gmx-users] ligand related problem
RINU KHATTRI
- [gmx-users] Wrong profile obtained in umbrella sampling tutorial
Victor Rosas Garcia
- [gmx-users] constrained bonds
marzieh dehghan
- [gmx-users] no output from rms
Mark Abraham
- [gmx-users] Gromacs 5.0.1 restart simulation
wh
- [gmx-users] Install gromacs 5.0.2,ERROR
Hooman Vahidi
- [gmx-users] gromacs installation
Amir Khan
- [gmx-users] gromacs installation
Amir Khan
- [gmx-users] Query in protein insertion in membrane
Priya Das
- [gmx-users] Different box volumes from gmxdump and g_energy
Johnny Lu
- [gmx-users] Gromacs 5.0.1 restart simulation
wh
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 10
wh
- [gmx-users] Performance of GPU Workstation (GPU selection)
mail at 2718-mail.de
- [gmx-users] default state of "energygrps" in .mdp file
Agnivo Gosai
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 11
wh
- [gmx-users] merging chains in gromos43a1p
Jayant James
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 12
wh
- [gmx-users] questions about normal mode analysis in gromacs
凌未风
- [gmx-users] Remove rotation from rmsd
Mikhail Yustanov
- [gmx-users] How can I analyze an interaction between protein and CU ions
Batdorj Batsaikhan
- [gmx-users] use of g_hbond
soumadwip ghosh
- [gmx-users] Umbrella Sampling continuation
Alexander Law
- [gmx-users] Errors about dihidral angle type 9 in free energy perturbation
Jianguo Li
- [gmx-users] g_spatial
pratibha kapoor
- [gmx-users] energy groups rerun from reduced xtc file
Harry Mark Greenblatt
- [gmx-users] g_covar + g_anaeig entropy calculation
Albert
- [gmx-users] (no subject)
Prajisha Sujaya
- [gmx-users] Umbrella Sampling continuation
Lalita Shaki
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15
soumadwip ghosh
- [gmx-users] use of g_hbond
soumadwip ghosh
- [gmx-users] charmm to gromacs
Rebeca García Fandiño
- [gmx-users] biasing potential replica exchang for polymer
leila salimi
- [gmx-users] MDP parameters for OPLS-aa + Verlet cutoff scheme
Jernej Zidar
- [gmx-users] using g_hbond between index gps of specific interest
soumadwip ghosh
- [gmx-users] Regarding parallel run in Gromacs 5.0
Bikash Ranjan Sahoo
- [gmx-users] adding a new residue into an existing force field?
marzieh dehghan
- [gmx-users] multinode issue
Éric Germaneau
- [gmx-users] Regarding Gromacs parallel run
Bikash Ranjan Sahoo
- [gmx-users] Re : using g_hbond between index gps of specific interest
soumadwip ghosh
- [gmx-users] using g_hbond between index gps of specific
soumadwip ghosh
- [gmx-users] Simulating Carbon nanotubes as finite systems in GROMACS
Sergio Manzetti
- [gmx-users] Structure downloads
Norman, Lucy
- [gmx-users] running g_tune_pme on stampede
Kevin Chen
- [gmx-users] A small Questions of umbrella samping
vg
- [gmx-users] how to scale epsilon parameters of Lennard-Jones term in .top file
周双艳
- [gmx-users] Regarding Gromacs 5.0 parallel installation
Bikash Ranjan Sahoo
- [gmx-users] A small Questions of umbrella samping
vg
- [gmx-users] Make DNA stay in the center of the box during Simulation
Hovakim Grabski
- [gmx-users] CNT simulation
Sergio Manzetti
- [gmx-users] Отв: Make DNA stay in the center of the box during Simulation
Justin Lemkul
- [gmx-users] Precision of xtc-precision
Johnny Lu
- [gmx-users] .itp file of choline molecule
soumadwip ghosh
- [gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?
周双艳
- [gmx-users] Problems with CO2-water simulation
sujithkakkat .
- [gmx-users] Error in protein insertion in bilipid layer
Priya Das
- [gmx-users] running solvate twice...
Harry Mark Greenblatt
- [gmx-users] Basic GROMACS questions
Simone Bolognini
- [gmx-users] slight correction...
Harry Mark Greenblatt
- [gmx-users] .itp file of choline molecule
soumadwip ghosh
- [gmx-users] trr file time/frame information
gromacs query
- [gmx-users] Basic GROMACS questions
Simone Bolognini
- [gmx-users] g_wham 4.67 version output query
Agnivo Gosai
- [gmx-users] Question on installation
Igor Shchechkin
- [gmx-users] conformational entropy
xy21hb
- [gmx-users] ProDrg
xy21hb
- [gmx-users] protein-ligand complex fatal error
Yaser Hosseini
- [gmx-users] Basic GROMACS questions
Simone Bolognini
- [gmx-users] Problems about the WALL used with NPT systems: possible bug?
xu zhijun
- [gmx-users] g_wham 4.6.7 version output query
Agnivo Gosai
- [gmx-users] Problems about the WALL used with NPT systems: possible bug?
xu zhijun
- [gmx-users] Protein distance with respect to box walls
James Lord
- [gmx-users] PMF and RDF
sujithkakkat .
- [gmx-users] Free energy calculation by MM_PBSA
Indu Kumari
- [gmx-users] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014
FyD
- [gmx-users] problem during energy minimization
soumadwip ghosh
- [gmx-users] Gromacs 5.0.3 released
Mark Abraham
- [gmx-users] Dihedral angle calculation in Gromacs
Johnny Lu
- [gmx-users] Your solvent group size (*) is not a multiple of *
Hassan Aaryapour
- [gmx-users] Possible bugs: Problems about the 12-6 WALL used with NPT systems.
xu zhijun
- [gmx-users] gromacs on GPU
Shaohao Chen
- [gmx-users] Regarding Gromacs 5.0.3 parallel computation
Bikash Ranjan Sahoo
- [gmx-users] Installation problem with Gromacs 5.0.2
PAULAMI CHATTERJEE
- [gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits
bipin singh
- [gmx-users] Problem with gmx-users mail list subscription
Elena Lilkova
- [gmx-users] Morse potential for Specific Group
Jackson Chief Elk
- [gmx-users] how to scale epsilon parameters of Lennard-Jones term in .top file
Shuangyan Zhou
- [gmx-users] use of g_densmap
soumadwip ghosh
- [gmx-users] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0?
Batdorj Batsaikhan
- [gmx-users] Segmentation fault error
Seyed Mojtaba Rezaei Sani
- [gmx-users] Maximun time-step recommended in the grompp part for each system
Mario Fernández Pendás
- [gmx-users] xeon-phi and double precision
Johnny Lu
- [gmx-users] Segmentation fault error
Seyed Mojtaba Rezaei Sani
- [gmx-users] Using g_densmap
soumadwip ghosh
- [gmx-users] How to define the covalent bonds between ligand and protein
Bikash Ranjan Sahoo
- [gmx-users] Fwd: Question about GPU acceleration in GROMACS 5
Tomy van Batis
- [gmx-users] protein-ligand complex fatal error
Yaser Hosseini
- [gmx-users] trjconv precision lost from double to single conversion
Johnny Lu
- [gmx-users] pmetune and restarting
Johnny Lu
- [gmx-users] with 5.0: file INSTALL cannot find gmx
Jochen Hub
- [gmx-users] pdb2gmx atom not found
xy21hb
- [gmx-users] Segfault on energy minimization
Diego Muñoz G.
- [gmx-users] Fw: pdb2gmx atom not found
xy21hb
- [gmx-users] output dispersion correction and coul. recip. for energy groups
Yongchul Chung
- [gmx-users] adding hydrogen atoms into a POPC membrane
Carlos Navarro Retamal
- [gmx-users] Stop protein diffusion in simulation box to make a movie
Hassan Aaryapour
- [gmx-users] Need to Sort Out
Devender Arora
- [gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?
Christopher Neale
- [gmx-users] content of trr / xtc files + -b/-e flag question + tpr question
Eric Smoll
- [gmx-users] Problems with CO2-water simulation
sujithkakkat .
- [gmx-users] mdp file coarse grained simulation with cutoff-scheme =?utf-8?Q?=3D_?=Verlet
Carlos Navarro Retamal
- [gmx-users] trjconv during transfer of .trr
Johnny Lu
- [gmx-users] Walls and pressure coupling
Jingjie
- [gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?
Christopher Neale
- [gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09
Jason Hill
- [gmx-users] avx2 with gcc 4.8.3
Harry Mark Greenblatt
- [gmx-users] can you please add my email to the mailing list?
Vered Kunik
- [gmx-users] gromacs workshop in Europe during 2015
Vered Kunik
- [gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09
Jason Hill
- [gmx-users] 0 +- 0.5 bar ok?
Johnny Lu
- [gmx-users] Gromacs 5.0.4 released
Mark Abraham
- [gmx-users] parametrization of GABA for charmm27
jkrieger at mrc-lmb.cam.ac.uk
- [gmx-users] avx2 with gcc 4.8.3
Roland Schulz
- [gmx-users] Ions drifting
jani vinod
- [gmx-users] Steered molecular dynamics
Priya Das
- [gmx-users] GXT690 vs GTX Titan black
Albert
- [gmx-users] Add new residue to forcefield
fatemeh ramezani
- [gmx-users] send this as a post
Abid Channa
- [gmx-users] Converting Amber parameters to gromacs parameters
Carlos Navarro Retamal
- [gmx-users] g_hbond not running
antoni borysik
- [gmx-users] Renumber atom ids and charge group in topology (.itp)
Nash, Anthony
- [gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed
Mike Hanby
- [gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed
Roland Schulz
- [gmx-users] Question about water freezing when in contact to a solid surface
ramon
- [gmx-users] Silica monolayer with Martini force field
André Farias de Moura
- [gmx-users] fatal erroe in prorein-ligand comlex
Yaser Hosseini
- [gmx-users] GTX 980 benchmark
Hadházi Ádám
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74
Abid Channa
- [gmx-users] Force Field for protein in water
neha bharti
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74
Yaser Hosseini
- [gmx-users] Fw: Add new residue to oplsaa force field
fatemeh ramezani
- [gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified
Christopher Neale
- [gmx-users] Force between two groups of atoms
ibrahim khalil
- [gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09
Jason Hill
- [gmx-users] compiling for xeon phi
Johnny Lu
- [gmx-users] Amber missing psi dihedral at cationic N-terminus of protein/peptide?
Christopher Neale
- [gmx-users] g_mindist
James Lord
- [gmx-users] CG MD Simulation of DNA and PAMAM dendrimers
Doa Hawamdeh
- [gmx-users] PTM force field
Jianqing Xu
- [gmx-users] Add new residue to oplsaa force field
fatemeh ramezani
- [gmx-users] Pressure in gromacs
Sushma Yadav
- [gmx-users] Xeon Phi benchmark?
Albert
- [gmx-users] AMD GPUs
Szilárd Páll
- [gmx-users] How to change the multiplicity of a dihedral in FEP in Gromacs
bipin singh
- [gmx-users] Mplecular Dynamic simulation of DNA and PAMAM dendrimers
Doa Hawamdeh
- [gmx-users] Problem Simulating a protein with small peptides
Arash Firouzbakht
- [gmx-users] martinize.py: option for partly have elastic network on partly in the protein
shivangi nangia
- [gmx-users] how can i use acpype
Yaser Hosseini
- [gmx-users] Working on a GPU cluster with GROMACS 5
Ebert Maximilian
- [gmx-users] Preparing a silicon bulk
Kevin C Chan
- [gmx-users] Preparing a silicon bulk
Kevin C Chan
- [gmx-users] Atomtype ZN2+ not found
Shankar Prasad Kanaujia
- [gmx-users] BN parameters in MD
Kester Wong
- [gmx-users] Query regarding ligand topology
Priya Das
- [gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09
Jason Hill
- [gmx-users] Question about water freezing when in contact to a solid surface (ramon)
ramon
- [gmx-users] Preparing a silicon bulk
Kevin C Chan
- [gmx-users] Naughty Vacuum Bubble in our Vesicle!
Björn Sommer
- [gmx-users] Element naming format in .pdb file
Rajan Kumar
- [gmx-users] Pressure in gromacs
Narendra Kumar
- [gmx-users] Non-bonded interactions
Doa Hawamdeh
- [gmx-users] Preparing a silicon bulk
Kevin C Chan
- [gmx-users] Postdoctoral position at the KAUST
Luigi Cavallo
- [gmx-users] a question about Electric fields
BIRD
- [gmx-users] (no subject)
Doa Hawamdeh
- [gmx-users] PCA of crystal structures
neeru sharma
- [gmx-users] fluid flow
Katie Maerzke
- [gmx-users] minimal distance between periodic images
jinxin
- [gmx-users] Regarding Null free energy values in Free energy perturbation (bond force constant perturbation)
bipin singh
- [gmx-users] qm-mm calculation : Gromacs + cpmd
Nilesh Dhumal
- [gmx-users] Installing GTX 980 on linux - which distro should i use?
Carlos Navarro Retamal
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 97
jinxin
- [gmx-users] Illegal instruction flag raised in GMX 5.0.4
Jayant James
- [gmx-users] malloc error at mdrun step
Kalyan Reddy
- [gmx-users] Implicit and explicit solvation
neha bharti
- [gmx-users] Protein split with mindist
Tsjerk Wassenaar
- [gmx-users] calculation of H-bonds
soumadwip ghosh
- [gmx-users] Error in topology using g_x2top
Rajan Kumar
- [gmx-users] Pulling code
asasa qsqs
- [gmx-users] gmxcheck : Magic Number Error in XTC file (read 0, should be 1995)
Amit Kumawat
- [gmx-users] initial velocities
mah maz
- [gmx-users] Pulling code
asasa qsqs
- [gmx-users] length of beta sheet
pratibha kapoor
- [gmx-users] Questions about CO2.
sujithkakkat .
- [gmx-users] Pulling
asasa qsqs
- [gmx-users] dangling bond error no matter what pdb file I use
asasa qsqs
- [gmx-users] How to choose the best pose of ligand from the trajectory file?
Hassan Aaryapour
- [gmx-users] how to use gmx convert-tpr for GMX5.0.4
Smart Eagle
- [gmx-users] How to use gmx convert-tpr for GMX5.0.4
Smart Eagle
- [gmx-users] extracting velocities
mah maz
- [gmx-users] MMPBSA & GMXPBSA 2.1
Tom
- [gmx-users] conversion of amber outputs to gromacs
shahab shariati
- [gmx-users] How to plot a droplet radius profile as a function of z-direction?
Kester Wong
- [gmx-users] RDF calculation.
soumadwip ghosh
- [gmx-users] core dumped
elham tazikeh
- [gmx-users] Error during entropy calculation
bipin singh
- [gmx-users] charge distribution
elham tazikeh
- [gmx-users] core dumped
elham tazikeh
- [gmx-users] Fatal error during entropy calculation using g_anaeig
bipin singh
- [gmx-users] charge distribution
elham tazikeh
- [gmx-users] how to remove water molecule inside micelle?
Mina Hashemi
- [gmx-users] farticle demanding about Small-Molecule Topologies
elham tazikeh
- [gmx-users] how to remove water molecule inside micelle
ABEL Stephane 175950
- [gmx-users] -vsite hydrogen
h.alizadeh at znu.ac.ir
- [gmx-users] Obtaining PMF for change in domain position
Abhi Acharya
- [gmx-users] pdb information
elham tazikeh
- [gmx-users] Gromacs error regarding default gromos bond type and angle type
Negar Parvizi
- [gmx-users] -vsite hydrogen
Wojciech Kopeć
- [gmx-users] charge distribution
elham tazikeh
- [gmx-users] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)
Carlos Navarro Retamal
- [gmx-users] RDF does not reach 1 for bulk
Venkat Reddy
- [gmx-users] pdb information
elham tazikeh
- [gmx-users] box siz
mah maz
- [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 91
Jason Hill
- [gmx-users] Projection of trajectory onto PCs
tarak karmakar
- [gmx-users] All-atom vs United-atom force fields and hydrogen bonds
Jason Hill
- [gmx-users] Define a new group for protein-ligand system
Shima Arasteh
- [gmx-users] charge distriburion
elham tazikeh
- [gmx-users] How to plot a droplet radius profile as a function of z-directio
Kester Wong
- [gmx-users] Define a new group for protein-ligand complex system
Shima Arasteh
- [gmx-users] error while executing do_dssp program
Nizar Masbukhin
Last message date:
Wed Dec 31 21:08:30 CET 2014
Archived on: Wed Dec 31 21:08:32 CET 2014
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