Re: [gmx-users] make an index file of COM of lipid bilayer
On 7/16/13 5:30 AM, Shima Arasteh wrote: Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Index files can't specify positions, only atoms. In this case, you don't even need a special index group - just use the membrane. The pull code uses the COM of the selected group, so if you specify your membrane, mdrun knows to use its COM. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Make an index file
Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? Cheers, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 3:10 AM Subject: Re: [gmx-users] Make an index file On 4/28/12 2:06 PM, Peter C. Lai wrote: #2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? If it is a .pdb file, the standard residue name occupies 3 characters. Many files (including those from Tieleman) are distributed with such names. To the OP's original question - the commands you issue depend on what you're trying to achieve. What group do you need to create? -Justin -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains these: [ moleculetype ] ; Name nrexcl POPC 3 . . . . [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3800 It is the command I enter: # make_ndx -f em.gro -o index.ndx 0 System : 18056 atoms 1 Other : 6656 atoms 2 POP : 6656 atoms 3 Water : 11400 atoms 4 SOL : 11400 atoms 5 non-Water : 6656 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Make an index file
On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title= NVT equilibration for POPC define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= POPC SOL; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t= 0.10.1; time constant, in ps ref_t= 323 323; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- 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] Make an index file
Dear MArkWow, That was kind of you. I appreciate you. Ok, I will try it. Thanks, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing list gmx-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-- 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] Make an index file
Dear Mark, Wow, That was kind of you. I appreciate you. Ok, I will try it. Thanks,Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing list gmx-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-- 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] Make an index file
#2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains these: [ moleculetype ] ; Name nrexcl POPC 3 . . . . [ system ] ; name POPC in water [ molecules ] ; namenumber POPC 128 SOL 3800 It is the command I enter: # make_ndx -f em.gro -o index.ndx 0 System : 18056 atoms 1 Other : 6656 atoms 2 POP : 6656 atoms 3 Water : 11400 atoms 4 SOL : 11400 atoms 5 non-Water : 6656 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge -- 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] Make an index file
On 4/28/12 2:06 PM, Peter C. Lai wrote: #2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? If it is a .pdb file, the standard residue name occupies 3 characters. Many files (including those from Tieleman) are distributed with such names. To the OP's original question - the commands you issue depend on what you're trying to achieve. What group do you need to create? -Justin -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains these: [ moleculetype ] ; Name nrexcl POPC 3 . . . . [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3800 It is the command I enter: # make_ndx -f em.gro -o index.ndx 0 System : 18056 atoms 1 Other : 6656 atoms 2 POP : 6656 atoms 3 Water : 11400 atoms 4 SOL : 11400 atoms 5 non-Water : 6656 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
