Re: [gmx-users] problem in running md simulation
Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] problem in running md simulation
Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing list
Re: [gmx-users] problem in running md simulation
On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. One should not make haphazard changes to cutoffs. They are part of the force field. Changing them without basis can invalidate the force field model. -Justin bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior
Re: [gmx-users] problem in running md simulation
Oh, I am sorry That is right. But its difficult to find The specific cutoff values to be used for different protocols of cutoff, switch and shift.. different values are stated in different papers.. And original force field paper (eg OPLSAA) does not explicitly specify these values. Any references regarding this will be helpful for the users. bye kavya On Fri, Nov 16, 2012 at 8:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. One should not make haphazard changes to cutoffs. They are part of the force field. Changing them without basis can invalidate the force field model. -Justin bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in ananyachatter...@iiserkol.ac.**inananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not,
[gmx-users] problem in running md simulation
Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem in running md simulation
I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
