[gmx-users] How to run MD with longer recording interval to reduce the file size?
Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Hello, Normally, you don't need to write out the force and velocity, then you can set nstfout and nstvout as ZERO, then only the coordinates will be written out in a xtc file. If you don't care about waters, then you can also set xtc-grps as a group without waters and counterions. Best, Qinghua On 12/15/2017 11:33 AM, ZHANG Cheng wrote: Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
On 12/15/17 7:34 AM, ZHANG Cheng wrote: Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? nstenergy is the frequency of writing energy terms to the .edr file. It has no effect on the .trr, which is only impacted by nstxout (coordinates), nstvout (velocities), and nstfout (forces). Also, how to set xtc-grps as a group? It's compressed-x-grps. -Justin The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Hello, Here is the settings I used in the mdp file, you may consider it. nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout = 500 ; xtc compressed trajectory output every 2 ps nstenergy = 500 ; save energies every 2 ps nstlog = 500 ; update log file every 2 ps xtc-grps = Protein energygrps = Protein Non-Protein I also checked the manual, I didn't find the option nstxtcout, maybe it is used in the old version of Gromacs, but I guess it is still used in the new version. You may go through the manual and set it properly. All the best, Qinghua On 12/15/2017 01:34 PM, ZHANG Cheng wrote: Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"? 3) Do you mean using "compressed-x-grps=Protein" will set xtc-grps as a group without waters and counterions? -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 08:34 PM To: "ZHANG Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"; Subject: Re: How to run MD with longer recording interval to reduce the file size? Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Hello, Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? Yeah, you can add that line, or you can leave it be, the default is set as ZERO. 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"? It depends on how many configurations you want to write out. 5 might be a little to big if you just run short simulations. 3) Do you mean using "compressed-x-grps=Protein" will set xtc-grps as a group without waters and counterions? This also depends on what system you are simulating. If it is a protein system, then it should be OK, if it is a protein+ ligand or protein + DNA system, then you need to make the index file yourself with gmx make_ndx. Best, Qinghua -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 08:34 PM To: "ZHANG Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"; Subject: Re: How to run MD with longer recording interval to reduce the file size? Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: How to run MD with longer recording interval to reduce the file size? Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you.
