May 2007 Archives by thread
Starting: Tue May 1 01:12:41 CEST 2007
Ending: Thu May 31 18:47:46 CEST 2007
Messages: 707
- [gmx-users] use of -dt
bmmothan at ucalgary.ca
- [gmx-users] Initial Temperature
George Abadir
- [gmx-users] Can I add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions.
intelandamd
- [gmx-users] Pressure Coupling
George Abadir
- [gmx-users] HG at active site of alcohol dehydrogenase
Mahnam
- [gmx-users] energy of each residue??
Pradeep Kota
- [gmx-users] Regarding DOPC parameters
naga raju
- [gmx-users] Electrostatic potential
Georgios Patargias
- [gmx-users] Restarting a crashed MD run
bmmothan at ucalgary.ca
- [gmx-users] Wall feature
Luis Moux
- [gmx-users] Workshop on Molecular Docking, Complexity and Optimization
Carsten Baldauf
- [gmx-users] g_energy sum
Berk Hess
- [gmx-users] MD runs and subsequent error
Joern Lenz
- [gmx-users] l-bfgs
Sona Aramyan
- [gmx-users] rotational fit in XY plane only
Dr Itamar Kass
- [gmx-users] topology for nitrosylated cysteine?
Daniel Rigden
- [gmx-users] GROMACS Wiki
Moore, Jonathan (J)
- [gmx-users] cutting out a portion of a crystal using triclinic box
Andrea Robben Browning
- [gmx-users] Compressibility issue - real concern
Jones de Andrade
- [gmx-users] (no subject)
Zuzana Benkova
- [gmx-users] PVT-simulation
Jiang ran
- [gmx-users] Temperature increase
Zuzana Benkova
- [gmx-users] PVT-simulation
Jiang ran
- [gmx-users] How to preserve the original sequence number
Stéphane Téletchéa
- [gmx-users] Unable to swith from NVT to NPT
Stéphane Téletchéa
- [gmx-users] xmgrace
Michal Walczak
- [gmx-users] Carbon Nanotube-Protein interaction
George Abadir
- [gmx-users] RE: Energy conservation in collision
Janne Hirvi
- [gmx-users] Energy conservation of crystal surface
Janne Hirvi
- [gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Arun kumar
- [gmx-users] Question on [ angles ] in topology file?
Chze Ling Wee
- [gmx-users] g_sas
Arthur Roberts
- [gmx-users] Positive Potential Energy
George Abadir
- [gmx-users] double-checking
V. Tanchuk
- [gmx-users] Re: gmx-users Digest, Vol 37, Issue 18
Arun kumar
- [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Arun kumar
- [gmx-users] Document about file input format to GROMACS program?
root
- [gmx-users] Positive and negative ions move in the same direction under a constant electric field?
林揚善
- [gmx-users] Energy conservation of crystal surface (specification)
Janne Hirvi
- [gmx-users] Targeted Molecular dynamics
Olivier Perin
- [gmx-users] Re: Energy conservation of crystal surface (specification)
Janne Hirvi
- [gmx-users] Regarding conversion of C6/C12 parameters in .itp file
naga raju
- [gmx-users] Regarding DOPC lipid parameters
naga raju
- [gmx-users] Very large fluctuations in dg/dl
Patrick Fuchs
- [gmx-users] Problems using grompp and amber force field
root
- [gmx-users] Cys-Cys Bond
fulya caglar
- [gmx-users] Problems using grompp and amber force field
TJ Piggot
- [gmx-users] Very large fluctuations in dg/dl
John D. Chodera
- [gmx-users] Problems using grompp and amber force field
root
- [gmx-users] (no subject)
vijaya subramanian
- [gmx-users] Visualization Problem
George Abadir
- [gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms
kong.winter
- [gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon
naga raju
- [gmx-users] Residue 'SIA' not found in residue topology database
kong.winter
- Fwd: [gmx-users] Fatal error:Atom S in residue TYR 2 not found
Tsjerk Wassenaar
- [gmx-users] bonus of MediaWiki
Mark Abraham
- [gmx-users] afm pull rate and pull info conflict
M.N. Manoj
- [gmx-users] Trjconv: reducing frames and Time issue
bmmothan at ucalgary.ca
- [gmx-users] Trjconv: reducing frames and Time issue
Alan Dodd
- [gmx-users] Human Serum Albumin problem
George Abadir
- [gmx-users] change the ligand in pdb file
Rui Li
- [gmx-users] eigenvectors in eigenvec.trr file
sunita at chem.iitb.ac.in
- [gmx-users] Parameter QMcharge does not work with Gromacs-CPMD
Christian Seifert
- [gmx-users] charge
pkmukher
- [gmx-users] nst option in g_cluster seems to be not working
sunita at chem.iitb.ac.in
- [gmx-users] how to use demux.pl for REMD analysis
N-J.M. Macaluso
- [gmx-users] cosine content
sunita at chem.iitb.ac.in
- [gmx-users] Parameterizing a force field
Lee-Ping
- [gmx-users] change the ligand in pdb file
Rui Li
- [gmx-users] problem with grompp and atomtype
Anna Marabotti
- [gmx-users] Question on analyzing REMD simulation
N-J.M. Macaluso
- [gmx-users] EM steep Total Energy
Claus Valka
- [gmx-users] fwspider and drug-enzyme tutorials
John E. Kerrigan
- [gmx-users] Where to start ? Gmx Newb !!
I BioKid
- [gmx-users] grompp atomtype problem
John E. Kerrigan
- [gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon
Chris Neale
- [gmx-users] Creating topology file for TBA cation using OPLS force field
Andrey A. Koverga
- [gmx-users] Re: Parameterizing a force field (Mark Abraham)
Lee-Ping
- [gmx-users] error estimates of free energy calculations
Jeroen van Bemmelen
- [gmx-users] problem with freeze-group : Large VCM
jagannath mondal
- [gmx-users] CNT-protein interaction
George Abadir
- [gmx-users] grompp error for customized topology
singh
- [gmx-users] Cannot find fftw3f
Omovie, Sheyore John
- [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Nicolas Sapay
- [gmx-users] suggest small revision to genbox
David Mobley
- [gmx-users] CNT Potassium doping with GROMACS
George Abadir
- [gmx-users] Error while running MD in DMSO!
Anil Kumar
- [gmx-users] Error while running grompp for em (MD) in Urea
Anil Kumar
- [gmx-users] area for DOPC bilayer
Justin MacCallum
- [gmx-users] Re : Positive and negative ions move in the same direction under a constant electric field?
林揚善
- [gmx-users] energy minimization of POPC crash
Shan shan Qin
- [gmx-users] protein in popc
mahbubeh zarrabi
- [gmx-users] about counterions
Rui Li
- [gmx-users] How to read xtc file?
Hu Zhongqiao
- [gmx-users] Ligand Parameters
Justin Lemkul
- [gmx-users] TREMD in development version
N-J.M. Macaluso
- [gmx-users] question about g_rmsdist
Fabrizio Mancinelli
- [gmx-users] ci variable range error in parallel but NOT in serial
dtmirij
- [gmx-users] turning off output of dgdl.xvg and VCM messages?
David Mobley
- [gmx-users] protein in popc
Chris Neale
- [gmx-users] Re: How to read xtc file?
Hu Zhongqiao
- [gmx-users] about counterions
Rui Li
- [gmx-users] Call for abstracts: Molecular Docking, Complexity, and Optimization. An ECCS 2007 Satellite Conference.
Carsten Baldauf
- [gmx-users] new default value for emtol with gromacs 3.3???
Jennifer Rendell
- [gmx-users] lipid solvent
sebastien santini
- [gmx-users] same simulation, different results
Jim Fonseca
- [gmx-users] error estimates of free energy calculations
Jeroen van Bemmelen
- [gmx-users] gromacs-3.3.1 and gcc-4.1.2
Tuan A. Tran
- [gmx-users] lipid solvent
chris.neale at utoronto.ca
- [gmx-users] Calculating energies of amino acids in a protein using g_energy
abhigna polavarapu
- [gmx-users] amb2gmx code
godawr at rpi.edu
- [gmx-users] PBC problem
Mu Yuguang (Dr)
- [gmx-users] Calculating energies of peptides in protein uisng g_energy
abhigna polavarapu
- [gmx-users] using VMD with GROMACS trajectories
Mark Abraham
- [gmx-users] top
mahbubeh zarrabi
- [gmx-users] Gromacs on Xserver G5 /MPI
abelius
- [gmx-users] compatibility of MOPAC charges with GROMACS ?
Daniel Rigden
- [gmx-users] How to use different reference structures for g_covar and g_anaeig
sridhar at cdfd.org.in
- [gmx-users] Error while doing EM in DMSO.
Anil Kumar
- [gmx-users] top
chris.neale at utoronto.ca
- [gmx-users] Gromacs on Xserver G5 /MPI
Warner Yuen
- [gmx-users] SGI Altix stack traceback
Aline Rossi
- [gmx-users] NOC 3.0 is released
mchen2 at mailer.fsu.edu
- [gmx-users] water only
Liqun He
- [gmx-users] gromacs future development guidelines?
Jones de Andrade
- [gmx-users] Re: Error while doing EM in DMSO.
Anil Kumar
- [gmx-users] error in topology file generation
Archana Chavan
- [gmx-users] Compiling Gromacs on 64 bit windows platform...
Kedar Potdar
- [gmx-users] FEP with real or dummy charges?
Georgios Patargias
- [gmx-users] how to increase the number of
Afonso Duarte
- [gmx-users] question about g_rmsdist II
Fabrizio Mancinelli
- [gmx-users] bondtype 5
Nicolas Schmidt
- [gmx-users] problem with genion
OZGE ENGIN
- [gmx-users] Calculate individual force between each atom pair
WU Yanbin
- [gmx-users] initial configuration problems and energy minimization
Arun kumar
- [gmx-users] energy minimization - double precision
Pradeep Kota
- [gmx-users] glibc error with g_density (only for some cases)
Arun kumar
- [gmx-users] zirconia
pushyami atluri
- [gmx-users] Language & manners on the list
lindahl at sbc.su.se
- [gmx-users] Testing Gromacs
Kedar Potdar
- [gmx-users] atom types @ bonded parameters
Francesco Pietra
- [gmx-users] how to increase the number of
Afonso Duarte
- [gmx-users] custom water model in gromacs
Diamantis Sellis
- [gmx-users] gromacs-antechamber-gaff
Francesco Pietra
- [gmx-users] energy minimization - double precision
Dr Itamar Kass
- [gmx-users] antechamber installation
Francesco Pietra
- [gmx-users] regarding zirconia
pushyami atluri
- [gmx-users] zirconia agen
pushyami atluri
- [gmx-users] Two polypeptides in one box
Sheyore Omovie
- [gmx-users] Two polypeptides in one box
Yang Ye
- [gmx-users] ci variable range error in parallel but NOT in serial
dtmirij
- [gmx-users] Error with Energy minimisation
Sheyore Omovie
- [gmx-users] Polarizability
Jones de Andrade
- [gmx-users] Two polypeptides in one box
Yang Ye
- [gmx-users] What molecule generator should be used if using GROMOS Force Field?
WU Yanbin
- [gmx-users] pH
Dmitriy Golubovsky
- [gmx-users] Re: gmx-users Digest, Vol 37, Issue 73
Dmitriy Golubovsky
- [gmx-users] Re: Calculate individual force between each atom pair
WU Yanbin
- [gmx-users] readxtc can not get coordinates without jump?
Hu Zhongqiao
- [gmx-users] REMD log files
N-J.M. Macaluso
- [gmx-users] Strategy for chaining jobs using different mdp parameters (long)
Stéphane Téletchéa
- [gmx-users] Strange error from my simulation
Stéphane Téletchéa
- [gmx-users] fatal error grompp !
Philippe Reymond
- [gmx-users] How to check memoryuse limit?
Alif M Latif
- [gmx-users] (no subject)
jyoung
- [gmx-users] problem with position-restrained dynamics of a charged system
OZGE ENGIN
- [gmx-users] problem with position-restrained dynamics of a charged system
OZGE ENGIN
- [gmx-users] problem with position-restrained dynamics of a charged system
OZGE ENGIN
- [gmx-users] g_dist problems
Edvin Erdtman
- [gmx-users] problem with position-restrained dynamics of a charged system
OZGE ENGIN
- [gmx-users] problem with position-restrained dynamics of a charged system
OZGE ENGIN
- [gmx-users] gettin a amorhous system??
pushyami atluri
- [gmx-users] bootstrap problem
tomas.itsx at centrum.cz
- [gmx-users] zirconia
pushyami atluri
- [gmx-users] drug-enzyme tutorial
John Kerrigan
- [gmx-users] Surfactant molecules missing after genbox
Alif M Latif
- [gmx-users] "Range checking error" issue
Matteo Guglielmi
- [gmx-users] how to avoid pdb2gmx from deleting duplicates?
Alif M Latif
- [gmx-users] how to find out the average running structure
Sonali
- [gmx-users] Re: readxtc can not get coordinates without jump?
Hu Zhongqiao
- [gmx-users] fatal error
Sonali
- [gmx-users] Restarting AFM pulling
Semen Esilevsky
- [gmx-users] do_dssp for many peptides
Volker Knecht
- [gmx-users] atom type not found error
mahbubeh zarrabi
- [gmx-users] pdb2gmx -merge option take a *very* long time, and doesn't work ...
Stéphane Téletchéa
- [gmx-users] bootstrap problem
tomas.itsx at centrum.cz
- [gmx-users] make gmx_disre.c error
tomas.itsx at centrum.cz
- [gmx-users] (no subject)
ZhouLong Zhang
- [gmx-users] Re: Re: do_dssp for many peptides
Volker Knecht
- [gmx-users] do_dssp: main chain
Volker Knecht
- [gmx-users] g_angle dihedrals
Robert fiske
- [gmx-users] hacked...
David Mobley
- [gmx-users] Constraining N-H and H-H bonds in ammonium via SETTLE?
John D. Chodera
- [gmx-users] Specified frame doesn't exist or file not seekable
Sonali
- [gmx-users] pulling with dodecahedral box
Mareike Zink
- [gmx-users] BUG!!! AFM pulling/Constraint
Jiang ran
- [gmx-users] free energy tutorial results
Robert fiske
- [gmx-users] free energy tutorial results
Jeroen van Bemmelen
- [gmx-users] qm mm and charges in GMX!
Samuel Silva Pita
- [gmx-users] cg error
Alif M Latif
- [gmx-users] Regarding downloading make_hole program
naga raju
- [gmx-users] Tutorials
TK.Jiji
- [gmx-users] Wiki online
David van der Spoel
- [gmx-users] Regarding downloading make_hole program
naga raju
- [gmx-users] Stuck ...
chris.neale at utoronto.ca
- [gmx-users] qm mm and charges in GMX!
Samuel Silva Pita
- [gmx-users] Problems with forcefield amber99 in Gromacs
bo yang
- [gmx-users] A special invitation to join Batchmates.com
Sonali Priyadarshini
- [gmx-users] GROMACS not scaling well with Core4 Quad technology CPUs
Trevor Marshall
- [gmx-users] Re: ci barely out of bounds
chris.neale at utoronto.ca
- [gmx-users] searching bugzilla
chris.neale at utoronto.ca
- [gmx-users] Total energy with different energy groups
Daniel Cheong
- [gmx-users] removing a water molecule
Ragothaman Yennamalli
- [gmx-users] calculation of distance , angle ,dihedral
job560 at sohu.com
- [gmx-users] BFGS in NMA calculations?
Jones de Andrade
- [gmx-users] simulation popc
mahbubeh zarrabi
- [gmx-users] simulation popc
Yang Ye
- [gmx-users] simulation popc
Yang Ye
- [gmx-users] Polypeptide interaction
Sheyore Omovie
- [gmx-users] A question about positiont constraint
yang zaixing
- [gmx-users] Question about DNA simulation
bo yang
- [gmx-users] 1-4 interaction between 160 and 164 at distance 1.573 which is larger than the 1-4 table size 1.000 nm
abhigna polavarapu
- [gmx-users] Question about DNA simulation, To: gmx-users at gromacs.org
Chris Neale
- [gmx-users] Question about DNA simulation
bo yang
- [gmx-users] Question about DNA simulation
bo yang
- [gmx-users] calculation of distance , angle ,dihedral
Alan Dodd
- [gmx-users] Re: ci barely out of bounds
Chris Neale
- [gmx-users] Question about DNA simulation
Chris Neale
- [gmx-users] Question about DNA simulation
bo yang
- [gmx-users] [Fwd: genion doubt]
Mark Abraham
- [gmx-users] How to avoid centering of solute by genbox
M.N. Manoj
- [gmx-users] Fatal error: Error: Too many iterations in routine JACOBI
Una Bjarnadottir
- [gmx-users] QMMM free energy
Robert fiske
- [gmx-users] finding the minimum energy conformation after a complete mdrum.
Subhrangshu Supakar
- [gmx-users] segmentation fault
Marius Retegan
- [gmx-users] pdb2gmx error
Alaguraj Veluchamy
- [gmx-users] Small detail for the gromacs signature ...
Stéphane Téletchéa
- [gmx-users] grompp popc
mahbubeh zarrabi
- [gmx-users] Stuck --> unstuck ...
Stéphane Téletchéa
- [gmx-users] about solvate
Rui Li
- [gmx-users] QMMM free energy
Robert fiske
- [gmx-users] PO4--- Ion Topology
Jason O'Young
- [gmx-users] dihedral .ndx format
Russell Green
- [gmx-users] Question about MD simulation
bo yang
- [gmx-users] segmentation fault
Marius Retegan
- [gmx-users] about solvate
Rui Li
- [gmx-users] RE: Avoid centering in genbox
Dallas B. Warren
- [gmx-users] g_sas and f_index
Mark Abraham
- [gmx-users] about solvate
Rui Li
- [Fwd: Re: [gmx-users] QMMM free energy]
Gerrit Groenhof
- [gmx-users] Re: Fatal error: Error: Too many iterations in routine JACOBI
Una Bjarnadottir
- [gmx-users] about CNT simulation
bo yang
Last message date:
Thu May 31 18:47:46 CEST 2007
Archived on: Thu Nov 14 12:03:37 CET 2013
This archive was generated by
Pipermail 0.09 (Mailman edition).