March 2006 Archives by author

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Starting: Wed Mar 1 00:10:54 CET 2006
Ending: Fri Mar 31 21:08:35 CEST 2006
Messages: 551

[gmx-users] phi-chi angle Vs time plot A.Rampioni
[gmx-users] Dihedral restraints STEVENAZZI ANDREA
R: [gmx-users] Dihedral restraints STEVENAZZI ANDREA
R: R: [gmx-users] Dihedral restraints STEVENAZZI ANDREA
[gmx-users] Re: Counterions: influence on protein Mark Abraham
[gmx-users] mdrun has different results with similar files Mark Abraham
[gmx-users] distance restraints problem Mark Abraham
[gmx-users] grompp single vs double precisions Mark Abraham
[gmx-users] grompp single vs double precisions Mark Abraham
[gmx-users] Installation problem in IBM pawer PC Mark Abraham
[gmx-users] grompp single vs double precisions Mark Abraham
[gmx-users] grompp single vs double precisions Mark Abraham
[gmx-users] mdrun in vacuum diverging? -- possibly due to nopbc? Mark Abraham
[gmx-users] cg and contraints error Mark Abraham
[gmx-users] Is there any problem of pme in GROMACS3.3? Mark Abraham
[gmx-users] Simulation interruption Mark Abraham
[gmx-users] Segmentation fault Mark Abraham
[gmx-users] Unnatural amino acid MD Mark Abraham
[gmx-users] Incorrect .top file numbering Mark Abraham
[gmx-users] Segmentation fault Mark Abraham
[gmx-users] Problems with the SHAKE-algorithm -> is a problem of energy conservation Mark Abraham
[gmx-users] problem going from cut-off to pme Mark Abraham
[gmx-users] problem going from cut-off to pme Mark Abraham
[gmx-users] problem going from cut-off to pme Mark Abraham
[gmx-users] Small V.S. Large simulation box. Mark Abraham
[gmx-users] Small V.S. Large simulation box. Mark Abraham
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Mark Abraham
[gmx-users] what is the -ter flag?? Mark Abraham
[gmx-users] compiling on fedora Mark Abraham
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 Mark Abraham
[gmx-users] pdb2gmx illegal instruction Mark Abraham
[gmx-users] How to calculate free energy for each residue in protein? Mark Abraham
[gmx-users] Question.. Mark Abraham
[gmx-users] FEP Mark Abraham
[gmx-users] lam on centrino duo? Mark Abraham
[gmx-users] opteron 2xdual core for MD Mark Abraham
[gmx-users] opteron 2xdual core for MD Mark Abraham
[gmx-users] Heating schemes Mark Abraham
[gmx-users] Re: Gromacs 3.3 and 3.2.1 Mark Abraham
[gmx-users] Error: relative constraint deviation after LINCS Mark Abraham
[gmx-users] error in pdb2gmx step Annie Albin
[gmx-users] error in pdb2gmx step Annie Albin
[gmx-users] Re: position of a molecule in a bilayer Kia Balali-Mood
[gmx-users] clearspeed processors Carsten Baldauf
[gmx-users] encad problems Alexander Benedix
[gmx-users] pdb2gmx atom not found Una Bjarnadottir
[gmx-users] pdb2gmx atom not found Una Bjarnadottir
[gmx-users] Sun T1000's, multi-core, hyper-threaded Christian Burisch
[gmx-users] Restart without energies Jordi Camps
[gmx-users] Questions on Binding Free Energy Calculations Rob Carlson
[gmx-users] Gromacs 3.3 manual Andrea Carotti
[gmx-users] Gromacs 3.3 manual Andrea Carotti
[gmx-users] AFM pulling Andrea Carotti
[gmx-users] How to install MPI version of Gromacs on a Linux Cluster Andrea Carotti
[gmx-users] Range checking error Gaurav Chopra
[gmx-users] Range Checking Error Gaurav Chopra
[gmx-users] Range Checking error Gaurav Chopra
[gmx-users] LINCS Warning using mdrun Gaurav Chopra
[gmx-users] Range Checking Error Gaurav Chopra
[gmx-users] Range Checking Error Gaurav Chopra
[gmx-users] Re: LINCS Warning using mdrun Gaurav Chopra
[gmx-users] Re: LINCS Warning using mdrun Gaurav Chopra
[gmx-users] pull code question Marino Convertino
[gmx-users] pull code bug? Marino Convertino
[gmx-users] gromacs manual Anthony Cruz
[gmx-users] Re: LINCS Warning using mdrun Grazia Daminelli
[gmx-users] Problem with DNA chain Marco Deriu
[gmx-users] ffG43a1.n2t Marco Deriu
[gmx-users] phi-chi angle Vs time plot Dhananjay
[gmx-users] Constraints Dhananjay
[gmx-users] error while concatenating .xtc files Alan Dodd
[gmx-users] pdb2gmx atom not found Alan Dodd
[gmx-users] pull.pdo AFM force Soren Enemark
[gmx-users] Re: Counterions: influence on protein Maxim Fedorov
[gmx-users] Re: Counterions: influence on protein dynamics. Maxim Fedorov
[gmx-users] Polarisable water topology / Ions Maxim Fedorov
[gmx-users] Re: gmx-users Digest, Vol 23, Issue 34 Maxim Fedorov
[gmx-users] Analysis programs and PBC. Anton Feenstra
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro Xiaobing Feng
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro (2) Xiaobing Feng
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro Xiaobing Feng
[gmx-users] Hessian instability Ignacio Rodriguez Fernandez
[gmx-users] Problems with the SHAKE-algorithm Björn Fischer
[gmx-users] Problems with the SHAKE-algorithm -> is a problem of energy conservation Björn Fischer
[gmx-users] distance restraints problem Jim Fonseca
Antw: [gmx-users] Problem with simulated annealing!!! Peter Friedel
[gmx-users] Compilation problem on SGI ORIGIN 3800 Patrick Fuchs
[gmx-users] Problem with simulated annealing!!! poornima Gajendrarao
Antw: [gmx-users] Problem with simulated annealing!!! poornima Gajendrarao
[gmx-users] Re: Problem with simulated annealing!!! poornima Gajendrarao
[gmx-users] Protein out of water box Prasad Gajula
[gmx-users] Re: Gromacs 3.3 and 3.2.1 Gale, Ella
[gmx-users] Villin Benchmarks grompp error (Please Help) Arindam Ganguly
[gmx-users] How to make drug for OPLSA ff compatiable Maik Goette
[gmx-users] How to make drug for OPLSA ff compatiable Maik Goette
[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS) Maik Goette
[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS) Maik Goette
[gmx-users] nucleic acis simulation Andrey V. Golovin
[gmx-users] installation problem about correl.h Linchen Gong
[gmx-users] installation problem about correl.h Linchen Gong
[gmx-users] Position of a molecule in a bilayer Rama Gullapalli
[gmx-users] Not enough ref_t and tau_t values! Florian Haberl
[gmx-users] 32 bit dual core or 64 bit single core? Florian Haberl
[gmx-users] Re: Re:double precision minimization with version 3.3 Florian Haberl
[gmx-users] Error: relative constraint deviation after LINCS Florian Haberl
[gmx-users] Error: relative constraint deviation after LINCS Florian Haberl
[gmx-users] clearspeed processors Florian Haberl
[gmx-users] Sun T1000's, multi-core, hyper-threaded Roger Hall
[gmx-users] compiling on fedora Joanne Hanna
[gmx-users] compiling with gcc Joanne Hanna
[gmx-users] Preformance on AMD X2! Mikko Hellgren
[gmx-users] need suggestion for building TMA Mikko Hellgren
[gmx-users] Request for PDB with the same label as in Gromocs topologies. Mikko Hellgren
[gmx-users] Request for PDB with the same label as in Gromocs topologies. Mikko Hellgren
[gmx-users] Re: g_energy average --- bug? Berk Hess
[gmx-users] output frequency to dgdl.xvg Berk Hess
[gmx-users] Energy conservation Janne Hirvi
[gmx-users] rlist in PME Janne Hirvi
[gmx-users] genbox problem Roman Holomb
[gmx-users] genbox overlap checking Roman Holomb
[gmx-users] Why my protein always falls out of the water box? Shanjie Huang
[gmx-users] How to generate average C-alpha fluctuation during MD of every AA residue? Shanjie Huang
[gmx-users] Re: How to generate average C-alpha fluctuation during MD of every AA residue? Shanjie Huang
[gmx-users] Ligand often slips out from the binding site in MD; is it natural? Shanjie Huang
[gmx-users] can not write a gro file without atom names Jochen Hub
[gmx-users] Why my protein always falls out of the water box? Jochen Hub
[gmx-users] LINCS Warning using mdrun Jochen Hub
[gmx-users] Parameters for OPLS Jochen Hub
[gmx-users] Re: LINCS Warning using mdrun Jochen Hub
[gmx-users] Re: LINCS Warning using mdrun Jochen Hub
[gmx-users] How to install MPI version of GROMACS on a LINUX CLUSTER Jochen Hub
[gmx-users] GAFF MAKOTO ISHIKAWA
[gmx-users] opteron 2xdual core for MD Jayant James Jayasundar
[gmx-users] opteron 2xdual core for MD Jayant James Jayasundar
[gmx-users] opteron 2xdual core for MD Jayant James Jayasundar
[gmx-users] Incorrect .top file numbering Ashutosh Jogalekar
[gmx-users] Unnatural amino acid MD Ashutosh Jogalekar
[gmx-users] Segmentation fault Ashutosh Jogalekar
[gmx-users] Incorrect .top file numbering Ashutosh Jogalekar
[gmx-users] Segmentation fault Ashutosh Jogalekar
[gmx-users] Phenylglycine parametrization in OPLS Ashutosh Jogalekar
[gmx-users] Problem with phenylglycine MD Ashutosh Jogalekar
[gmx-users] Not enough ref_t and tau_t values Ashutosh Jogalekar
[gmx-users] Not enough ref_t and tau_t values Ashutosh Jogalekar
[gmx-users] Dummy atoms for electrostatics calculation Bob Johnson
[gmx-users] Restarting a periodic simulated annealing run Bob Johnson
[gmx-users] Non-zero system charge Bob Johnson
[gmx-users] pdb2gmx illegal instruction Tom Joseph
[gmx-users] Error: relative constraint deviation after LINCS Tom Joseph
[gmx-users] Error: relative constraint deviation after LINCS Tom Joseph
[gmx-users] Error: relative constraint deviation after LINCS Tom Joseph
[gmx-users] methanol/water mixture with all atoms Yousung Jung
[gmx-users] mdrun in vacuum diverging? -- possibly due to nopbc? Yousung Jung
[gmx-users] structure factor Yousung Jung
[gmx-users] How to install MPI version of Gromacs on a Linux Cluster Shankar Prasad Kanaujia
[gmx-users] How to install MPI version of GROMACS on a LINUX CLUSTER Shankar Prasad Kanaujia
[gmx-users] How to Install MPI version of GROMACS on a LINUX CLUSTER Shankar Prasad Kanaujia
[gmx-users] disabling assembly loops Senthil Kandasamy
[gmx-users] cg and contraints error Sampo Karkola
[gmx-users] gromacs manual Itamar Kass
[gmx-users] Fw: TM protein, lipids, force field Itamar Kass
[gmx-users] Non-zero system charge Itamar Kass
[gmx-users] steered MD Kamil Khafizov
[gmx-users] Parameters for OPLS Kobi
[gmx-users] distance restraints problem Michal Kolinski
[gmx-users] pull.pdo AFM force Michal Kolinski
[gmx-users] FEP Michal Kolinski
[gmx-users] Wrong LJ energies on Apple Mac OS X with Myrinet Goran Krilov
[gmx-users] Wrong LJ energies on Apple Mac OS X with Myrinet Goran Krilov
[gmx-users] Specifying pair interactions Goran Krilov
[gmx-users] Hessian instability Tomas Kubar
[gmx-users] Installation problem in IBM pawer PC Dilraj Lama
[gmx-users] Installation problem in IBM pawer PC Dilraj Lama
[gmx-users] error in pdb2gmx step Per Larsson
[gmx-users] Counterions in DNA simulation Yu Kay Law
[gmx-users] GLUH problem Jason Lee
[gmx-users] the force field of GROMOS96 Erik Lindahl
[gmx-users] Gromacs3.3 Compilation on IBM powerpc Erik Lindahl
[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc Erik Lindahl
[gmx-users] installation problem about correl.h Erik Lindahl
[gmx-users] mpi problem Erik Lindahl
[gmx-users] pdb2gmx illegal instruction Erik Lindahl
[gmx-users] pdb2gmx illegal instruction Erik Lindahl
[gmx-users] open_xtc() returns zero Erik Lindahl
[gmx-users] opteron 2xdual core for MD Erik Lindahl
[gmx-users] Re: question about non-orthongonal box vectors in pdc Erik Lindahl
[gmx-users] Re: question about non-orthongonal box vectors in pdc Erik Lindahl
[gmx-users] SR coulomb and LR Coulomb Erik Lindahl
[gmx-users] SR Coulomb and LR Coulomb Erik Lindahl
[gmx-users] Not enough ref_t and tau_t values! Miguel Ortiz Lombardia
[gmx-users] Not enough ref_t and tau_t values! Miguel Ortiz Lombardia
[gmx-users] Not enough ref_t and tau_t values! Miguel Ortiz Lombardia
[gmx-users] Gromacs 3.3 manual Diane Lynch
[gmx-users] Not enough ref_t and tau_t values! MGiò
[gmx-users] Why my protein always falls out of the water box? MGiò
[gmx-users] error in pdb2gmx step MGiò
[gmx-users] error in pdb2gmx step MGiò
[gmx-users] Polarisable water topology / Ions Paul van Maaren
[gmx-users] Ligand moves out of box during EM steps Alberto Malvezzi
[gmx-users] kind advice needed Marie
[gmx-users] Fatal error!!!!!!!!!!!!!!!!!!!!! Marcelo Fabricio Masman
[gmx-users] Hi all! Marcelo Fabricio Masman
[gmx-users] pdb2gmx atom not found Marcelo Fabricio Masman
[gmx-users] Fatal error!!!! Marcelo Fabricio Masman
[gmx-users] mdrun has different results with similar files Mathieu, Jennifer J.
[gmx-users] pdb2gmx CA -> CA2+ or not? David Mathog
[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS) David Mathog
[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS) David Mathog
[gmx-users] First release, translation supporting PDB<->(AMBER, GROMACS) David Mathog
[gmx-users] Request for PDB with the same label as in Gromocs topologies. David Mathog
[gmx-users] g_energy average --- bug? Fernando Mattio
[gmx-users] Tau_t values Fernando Mattio
R: [gmx-users] Dihedral restraints David Mobley
[gmx-users] GAFF David Mobley
[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion David Mobley
[gmx-users] umbrella sampling of angles David Mobley
[gmx-users] installation problem about correl.h David Mobley
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 David Mobley
[gmx-users] Ligand moves out of box during EM steps David Mobley
[gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple David Mobley
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 David Mobley
[gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple David Mobley
[gmx-users] bugzilla David Mobley
[gmx-users] FEP David Mobley
[gmx-users] FEP David Mobley
[gmx-users] Request for PDB with the same label as in Gromocs topologies. David Mobley
[gmx-users] Error: relative constraint deviation after LINCS David Mobley
[gmx-users] FEP David Mobley
[gmx-users] Specifying pair interactions David Mobley
[gmx-users] Non-zero system charge David Mobley
[gmx-users] Non-zero system charge David Mobley
[gmx-users] SR coulomb and LR Coulomb Hector Martinez-Seara Monne
[gmx-users] SR coulomb and LR Coulomb Hector Martinez-Seara Monne
[gmx-users] output frequency to dgdl.xvg Moore, Jonathan (J)
[gmx-users] output frequency to dgdl.xvg Moore, Jonathan (J)
[gmx-users] g_hbond question Moore, Jonathan (J)
[gmx-users] g_hbond question Moore, Jonathan (J)
[gmx-users] g_hbond question Moore, Jonathan (J)
[gmx-users] Analysis programs and PBC. Daniela S. Mueller
[gmx-users] genbox overlap checking Daniela S. Mueller
[gmx-users] Villin Benchmarks grompp error (Please Help) Daniela S. Mueller
[gmx-users] g_hbond question Daniela S. Mueller
[gmx-users] g_hbond question Daniela S. Mueller
[gmx-users] pdb2gmx problem Daniela S. Mueller
[gmx-users] Decabe density Naser, Md Abu
[gmx-users] distance measurement Naser, Md Abu
[gmx-users] distance measurement Naser, Md Abu
[gmx-users] Re: FEP Chris Oostenbrink
[gmx-users] bugzilla Miguel Ortiz-Lombardia
[gmx-users] Fw: TM protein, lipids, force field P
[gmx-users] Re: Fw: TM protein, lipids, force field P
[gmx-users] FEP P
[gmx-users] FEP P
[gmx-users] FEP P
[gmx-users] FEP P
[gmx-users] internal vs external pressure Lisa M. Perez
[gmx-users] Restraining bilayer/water system Xavier Periole
[gmx-users] Restraining bilayer/water system Xavier Periole
[gmx-users] Restraining bilayer/water system Xavier Periole
[gmx-users] Restraining bilayer/water system Xavier Periole
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 Xavier Periole
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3: the energy file Xavier Periole
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 Xavier Periole
[gmx-users] Questions on Binding Free Energy Calculations Xavier Periole
[gmx-users] N-terminus type PRO-NH Nguyen Hoang Phuong
[gmx-users] umbrella sampling, deshuffling and version 3.3 Enrico Piccinini
[gmx-users] problem from 3.2 to 3.3 version Adriana Pietropaolo
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Adriana Pietropaolo
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Adriana Pietropaolo
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Adriana Pietropaolo
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Adriana Pietropaolo
[gmx-users] Protein out of water box Adriana Pietropaolo
[gmx-users] ligand in vacuum trajectories (PRODRG) Dariusz Plewczynski
[gmx-users] wham Guillem Portella
[gmx-users] Restart without energies Guillem Portella
[gmx-users] Re: gmx-users Digest, Vol 23, Issue 99 hayagreevan R
[gmx-users] (no subject) hayagreevan R
[gmx-users] SHAKEt Sekar Ramachandran
[gmx-users] (no subject) Ken Rotondi
[gmx-users] ffG43a1.rtp file error Ken Rotondi
[gmx-users] ffG43a1.rtp file error Ken Rotondi
[gmx-users] wham James Rustad
[gmx-users] Gromacs Developer Position Available MD-group Groningen S.J.Marrink
[gmx-users] Compiling MOPAC7/Gromacs3.3 --errors YOLANDA SMALL
[gmx-users] xtc files YOLANDA SMALL
[gmx-users] xtc files YOLANDA SMALL
[gmx-users] ligand in vacuum trajectories (PRODRG) Farid Sa'adedin
[gmx-users] Simulation interruption Farid Sa'adedin
[gmx-users] Restraining bilayer/water system Farid Sa'adedin
[gmx-users] Restraining bilayer/water system Farid Sa'adedin
[gmx-users] Restraining bilayer/water system Farid Sa'adedin
[gmx-users] Restraining bilayer/water system Farid Sa'adedin
[gmx-users] Restraining bilayer/water system Farid Sa'adedin
[gmx-users] hi Lars Schaefer
[gmx-users] negative delta-lambda values? Lars Schaefer
[gmx-users] 32 bit dual core or 64 bit single core? Beniamino Sciacca
[gmx-users] 32 bit dual core or 64 bit single core? Beniamino Sciacca
[gmx-users] 32 bit dual core or 64 bit single core? Beniamino Sciacca
[gmx-users] lam on centrino duo? Beniamino Sciacca
[gmx-users] lam on centrino duo? Beniamino Sciacca
[gmx-users] problem with VMD Beniamino Sciacca
[gmx-users] Electric Field in part of the system Shafrir, Yinon (NIH/NCI) [F]
[gmx-users] Is there any problem of pme in GROMACS3.3? Sui Shen
[gmx-users] question about non-orthongonal box vectors in pdc Michael Shirts
[gmx-users] Re: question about non-orthongonal box vectors in pdc Michael Shirts
[gmx-users] Delta_E´s in TI Method Mauricio Sica
[gmx-users] negative delta-lambda values? Mauricio Sica
[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion Simple
[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion Simple
[gmx-users] "Cannot allocate memory" by grompp Sandeep Somani
[gmx-users] "Cannot allocate memory" by grompp Sandeep Somani
[gmx-users] Electric Field in part of the system David van der Spoel
[gmx-users] Electric Field in part of the system David van der Spoel
[gmx-users] the manual David van der Spoel
[gmx-users] error while concatenating .xtc files David van der Spoel
[gmx-users] Tau_t values David van der Spoel
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro David van der Spoel
[gmx-users] "Cannot allocate memory" by grompp David van der Spoel
[gmx-users] Fatal error!!!!!!!!!!!!!!!!!!!!! David van der Spoel
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro David van der Spoel
[gmx-users] Hi all! David van der Spoel
Fwd: [gmx-users] Compiling MOPAC7/Gromacs3.3 --errors David van der Spoel
[gmx-users] Is there any problem of pme in GROMACS3.3? David van der Spoel
[gmx-users] Preformance on AMD X2! David van der Spoel
[gmx-users] Problems with the SHAKE-algorithm David van der Spoel
[gmx-users] mdrun in vacuum diverging? -- possibly due to nopbc? David van der Spoel
[gmx-users] Segmentation fault David van der Spoel
[gmx-users] more detailed problem from 3.2.1 to 3.3 version David van der Spoel
[gmx-users] genbox problem David van der Spoel
[gmx-users] more detailed problem from 3.2.1 to 3.3 version David van der Spoel
[gmx-users] pdb2gmx atom not found David van der Spoel
[gmx-users] g_clustsize problem David van der Spoel
[gmx-users] xtc files David van der Spoel
[gmx-users] xtc files David van der Spoel
[gmx-users] Range checking error David van der Spoel
[gmx-users] Re:g_clustsize problem David van der Spoel
[gmx-users] Range Checking Error David van der Spoel
[gmx-users] Range Checking Error David van der Spoel
[gmx-users] Problem with phenylglycine MD David van der Spoel
[gmx-users] GAFF David van der Spoel
[gmx-users] new rtp file generation David van der Spoel
[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion David van der Spoel
[gmx-users] Protein-Protein interaction using Generalized-Reaction-Field David van der Spoel
[gmx-users] Dihedral restraints David van der Spoel
R: [gmx-users] Dihedral restraints David van der Spoel
[gmx-users] disabling assembly loops David van der Spoel
[gmx-users] Gromacs 3.3 manual David van der Spoel
[gmx-users] pdb2gmx illegal instruction (core dumped) David van der Spoel
[gmx-users] pdb2gmx illegal instruction (core dumped) David van der Spoel
[gmx-users] gromacs manual David van der Spoel
[gmx-users] pdb2gmx illegal instruction David van der Spoel
[gmx-users] ffG43a1.n2t David van der Spoel
[gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple David van der Spoel
[gmx-users] bugzilla David van der Spoel
[gmx-users] How to generate average C-alpha fluctuation during MD of every AA residue? David van der Spoel
[gmx-users] lam on centrino duo? David van der Spoel
[gmx-users] Constraints David van der Spoel
[gmx-users] Wrong LJ energies on Apple Mac OS X with Myrinet David van der Spoel
[gmx-users] Heating schemes David van der Spoel
[gmx-users] Error: relative constraint deviation after LINCS David van der Spoel
[gmx-users] gromacs with carbohydrates David van der Spoel
[gmx-users] Error: relative constraint deviation after LINCS David van der Spoel
[gmx-users] distance measurement David van der Spoel
[gmx-users] question about dielectric constant calculation David van der Spoel
[gmx-users] Non-zero system charge David van der Spoel
[gmx-users] Electric Field in part of the system Viswanadham Sridhara
[gmx-users] internal vs external pressure Viswanadham Sridhara
[gmx-users] can not write a gro file without atom names Viswanadham Sridhara
[gmx-users] How can I ask a question?? Viswanadham Sridhara
[gmx-users] Not enough ref_t and tau_t values Viswanadham Sridhara
[gmx-users] problem with VMD Viswanadham Sridhara
[gmx-users] Re: Problem with simulated annealing!!! Viswanadham Sridhara
[gmx-users] inclusion complexes of cyclodextrin and drugs Andreas Steffen
[gmx-users] inclusion complexes of beta-cyclodextrins and drugs Andreas Steffen
[gmx-users] gromacs with carbohydrates Andreas Steffen
[gmx-users] Gromacs 3.3 manual Stéphane Teletchéa
RES: [gmx-users] gromacs with carbohydrates Hugo Verli
[gmx-users] pull.pdo AFM force Emily Walton
[gmx-users] pull.pdo followup Emily Walton
[gmx-users] methanol/water mixture with all atoms Dallas B. Warren
[gmx-users] why my protein run out of the box? Dallas B. Warren
[gmx-users] Sun T1000's, multi-core, hyper-threaded Dallas B. Warren
[gmx-users] Restarting a periodic simulated annealing run Dallas B. Warren
[gmx-users] can not write a gro file without atom names Dallas B. Warren
[gmx-users] Polarisable water topology / Ions Dallas B. Warren
[gmx-users] problem with xtc in vmd Dallas B. Warren
[gmx-users] lam on centrino duo? Dallas B. Warren
[gmx-users] Error: relative constraint deviation after LINCS Dallas B. Warren
[gmx-users] Not enough ref_t and tau_t values! Tsjerk Wassenaar
[gmx-users] Not enough ref_t and tau_t values Tsjerk Wassenaar
[gmx-users] Computing RMSD for RNA structure Tsjerk Wassenaar
[gmx-users] Ligand moves out of box during EM steps Tsjerk Wassenaar
[gmx-users] Ligand moves out of box during EM steps Tsjerk Wassenaar
[gmx-users] Ligand moves out of box during EM steps Tsjerk Wassenaar
[gmx-users] Ligand moves out of box during EM steps Tsjerk Wassenaar
[gmx-users] Ligand moves out of box during EM steps Tsjerk Wassenaar
[gmx-users] About to introduce more than one protein in a box.... Tsjerk Wassenaar
[gmx-users] hi Tsjerk Wassenaar
[gmx-users] gromacs with carbohydrates Tsjerk Wassenaar
[gmx-users] Re: question about non-orthongonal box vectors in pdc Tsjerk Wassenaar
[gmx-users] Re: question about non-orthongonal box vectors in pdc Tsjerk Wassenaar
[gmx-users] Re: question about non-orthongonal box vectors in pdc Tsjerk Wassenaar
[gmx-users] distance measurement Tsjerk Wassenaar
[gmx-users] LINCS Warning using mdrun Steffen Wolf
[gmx-users] Re: LINCS Warning using mdrun Steffen Wolf
[gmx-users] Protein out of water box Steffen Wolf
[gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable Steffen Wolf
[gmx-users] the manual Rongliang Wu
[gmx-users] Rychaert-Belleman's dihedral Rongliang Wu
[gmx-users] keep atoms planar Rongliang Wu
[gmx-users] mpi problem Rongliang Wu
[gmx-users] grompp problem Rongliang Wu
[gmx-users] pdb2gmx problem Rongliang Wu
[gmx-users] chain construction Rongliang Wu
[gmx-users] Not enough ref_t and tau_t values X.Periole
[gmx-users] GLUH problem X.Periole
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 X.Periole
[gmx-users] How many boundary conditions in GMX? X.Periole
[gmx-users] Re: How to generate itp files of small moleclues for gromos96 force field X.Periole
[gmx-users] phi-chi angle Vs time plot X.Periole
[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3 X.Periole
[gmx-users] Heating schemes X.Periole
[gmx-users] Re: Re:double precision minimization with version 3.3 Yechun Xu
[gmx-users] Re:Re: Re: Re:double precision minimization with version 3.3 Yechun Xu
[gmx-users] grompp single vs double precisions Yang Ye
[gmx-users] grompp single vs double precisions Yang Ye
[gmx-users] grompp single vs double precisions Yang Ye
[gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro Yang Ye
[gmx-users] grompp single vs double precisions Yang Ye
[gmx-users] cg and contraints error Yang Ye
[gmx-users] Not enough ref_t and tau_t values! Yang Ye
[gmx-users] more detailed problem from 3.2.1 to 3.3 version Yang Ye
[gmx-users] problem going from cut-off to pme Yang Ye
[gmx-users] Small V.S. Large simulation box. Yang Ye
[gmx-users] Re: Small V.S. Large simulation box. Yang Ye
[gmx-users] 32 bit dual core or 64 bit single core? Yang Ye
[gmx-users] 32 bit dual core or 64 bit single core? Yang Ye
[gmx-users] calculation without box Yang Ye
[gmx-users] SHAKEt Yang Ye
[gmx-users] xtc files Yang Ye
[gmx-users] How 2 remove these warnings Yang Ye
[gmx-users] Re: LINCS Warning using mdrun Yang Ye
R: R: [gmx-users] Dihedral restraints Yang Ye
[gmx-users] Re: [gmx-developers] REMD based on prot pot ener: FINAL? Yang Ye
[gmx-users] Restraining bilayer/water system Yang Ye
[gmx-users] Restraining bilayer/water system Yang Ye
[gmx-users] Drug-Enzyme simulation Yang Ye
[gmx-users] Restraining bilayer/water system Yang Ye
[gmx-users] Restraining bilayer/water system Yang Ye
[gmx-users] mpi problem Yang Ye
[gmx-users] Error: relative constraint deviation after LINCS Yang Ye
[gmx-users] problem going from cut-off to pme Yiannis
[gmx-users] problem going from cut-off to pme Yiannis
[gmx-users] problem going from cut-off to pme Yiannis
[gmx-users] problem going from cut-off to pme Yiannis
[gmx-users] Small V.S. Large simulation box. Yinghong
[gmx-users] Re: Small V.S. Large simulation box. Yinghong
[gmx-users] Gromacs3.3 Compilation on IBM powerpc Yinghong
[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc Yinghong
[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc Yinghong
[gmx-users] How many boundary conditions in GMX? Yinghong
Fwd: [gmx-users] Compiling MOPAC7/Gromacs3.3 --errors Dong YuHui
[gmx-users] About to introduce more than one protein in a box.... Absalom Zamorano
[gmx-users] pdb2gmx illegal instruction Dongsheng Zhang
[gmx-users] pdb2gmx illegal instruction (core dumped) Dongsheng Zhang
[gmx-users] pdb2gmx illegal instruction (core dumped) Dongsheng Zhang
[gmx-users] pdb2gmx illegal instruction Dongsheng Zhang
[gmx-users] pdb2gmx illegal instruction Dongsheng Zhang
[gmx-users] pdb2gmx illegal instruction Dongsheng Zhang
[gmx-users] question about dielectric constant calculation Lei Zhou
[gmx-users] How to generate itp files of small moleclues for gromos96 force field Shulin Zhuang
[gmx-users] Re: How to generate itp files of small moleclues for gromos96 force field Shulin Zhuang
[gmx-users] How to Install MPI version of GROMACS on a LINUX CLUSTER Shulin Zhuang
[gmx-users] g_clustsize problem Wang Zhun
[gmx-users] Re:g_clustsize problem Wang Zhun
[gmx-users] Re:g_clustsize problem Wang Zhun
[gmx-users] question about exploding shensui830720 at aim.com
[gmx-users] why my protein run out of the box? shensui830720 at aim.com
[gmx-users] FEP paloureiro at biof.ufrj.br
[gmx-users] FEP paloureiro at biof.ufrj.br
[gmx-users] dihedral PCA paloureiro at biof.ufrj.br
[gmx-users] Cannot allocate memory problem during genion sunita at chem.iitb.ac.in
[gmx-users] Contribution to total potential energy given by protein in PME md pascal.baillod at epfl.ch
[gmx-users] SR Coulomb and LR Coulomb pascal.baillod at epfl.ch
[gmx-users] mpi problem bfmilne at ff.up.pt
[gmx-users] Re: Problem with simulated annealing!!! bfmilne at ff.up.pt
[gmx-users] the force field of GROMOS96 jiqing
[gmx-users] Simulated annealing MD chandran karunakaran
[gmx-users] Bond type for GROMOS !! ritwik kavathekar
[gmx-users] Re: g_energy average --- bug? pim lists
[gmx-users] How to calculate free energy for each residue in protein? lx
[gmx-users] Manual 3.3 paolo marracino
[gmx-users] hi santosh naik
[gmx-users] ligand in vacuum trajectories (PRODRG) raja
[gmx-users] How to make drug for OPLSA ff compatiable raja
[gmx-users] How to make drug for OPLSA ff compatiable raja
[gmx-users] Drug-Enzyme simulation raja
[gmx-users] Error : Molecule type redefined raja
[gmx-users] Computing RMSD for RNA structure raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Solvent accessbility of ligand in RNA raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Ligand moves out of box during EM steps raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] Error: relative constraint deviation after LINCS raja
[gmx-users] error while concatenating .xtc files manmohan singh
[gmx-users] Restraining bilayer/water system fsaadedi at staffmail.ed.ac.uk
[gmx-users] Restraining bilayer/water system fsaadedi at staffmail.ed.ac.uk
[gmx-users] topology for iron dicitrate syma
[gmx-users] How 2 remove these warnings Richa taimni
[gmx-users] problem with xtc in vmd smilidon theking
[gmx-users] rigid toluene gromacs at urp.dk
[gmx-users] open_xtc() returns zero chris.neale at utoronto.ca
[gmx-users] Testing nonbonded list update time chris.neale at utoronto.ca
[gmx-users] How to use genbox to add ions or other molecules chris.neale at utoronto.ca
[gmx-users] Could anybody post a sample.mdp for protein-membrane-aqueous simulation ? liu xin
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] grompp single vs double precisions rob yang
[gmx-users] calculation without box rob yang
[gmx-users] calculation without box rob yang
[gmx-users] oplsaa2005? rob yang
[gmx-users] ffG43a1.rtp file error rob yang
[gmx-users] Theory about steepest descent and conjugate gradient. zazeri
[gmx-users] Protein-Protein interaction using Generalized-Reaction-Field 亀田倫史
[gmx-users] GAFF 日産化学　石川誠
[gmx-users] GAFF 日産化学　石川誠
[gmx-users] [RE]Welcome to the "gmx-users" mailing list (Digest mode) 안세나
[gmx-users] [RE]Welcome to the "gmx-users" mailing list (Digest mode) 안세나
[gmx-users] new rtp file generation 안세나
[gmx-users] How can I ask a question?? 안세나
[gmx-users] question for rtpfile of liganded myoglobin 안세나
[gmx-users] what is the -ter flag?? 안세나
[gmx-users] more than two pulling groups 안세나
[gmx-users] for pulling groups 안세나
[gmx-users] Please answer for this question for pulling groups 안세나
[gmx-users] pulling code problem. 안세나
[gmx-users] Question.. 안세나
[gmx-users] help-pulling groups 안세나

Last message date: Fri Mar 31 21:08:35 CEST 2006
Archived on: Thu Nov 14 12:02:46 CET 2013

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