[gmx-users] Equilibration using position restraints in NPT
Neha Gandhi
n.gandhiau at gmail.com
Sun Oct 8 23:29:54 CEST 2017
Thank you Mark.
The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and
solvate using spc216.gro.
How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?
> Message: 1
> Date: Sun, 8 Oct 2017 23:38:58 +1000
> From: Neha Gandhi <n.gandhiau at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
> <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title = OPLS Lysozyme NPT equilibration
> define = -DPOSRES_CNT ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 500000 ; 2
> dt = 0.001 ; 2 fs
> ; Output control
> nstxout = 5000 ; save coordinates every 1.0 ps
> nstvout = 5000 ; save velocities every 1.0 ps
> nstenergy = 5000 ; save energies every 1.0 ps
> nstlog = 5000 ; update log file every 1.0 ps
> ;energygrps = Protein CNT Water NA
> ; Bond parameters
> continuation = yes ; Restarting after NVT
> 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 = Berendsen ; modified Berendsen
> thermostat
> tc-grps = CNT Water ; two coupling groups - more accurate
> tau_t = 0.2 0.2 ; time constant, in ps
> ref_t = 310 310 ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl = Berendsen ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box
> vectors
> tau_p = 5.0 ; 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
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 8 Oct 2017 22:34:21 +0530
> From: Dilip H N <cy16f01.dilip at nitk.edu.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regarding charges for atoms in a molecule
> Message-ID:
> <CAD6GXy07bfJ8BMOdi68a6rjkvf-tTF9kWF_VroK9nKfVdDQ-wA at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
> ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
> abc.gro command.
> 1] In the topology file, the charges for each atom are assigned. from where
> are these charges assigned..?? is it from the .rtp file, itp file..??
>
> 2] If so, I compared the charges in the generated topology file and in the
> merged.rtp file, but the charges are different in both the files...
>
> 3] I even checked in the ffnonbonded.itp file, but here for all the atom
> types the charges are 0.00 only...(why is this so...??)
>
> So, from where (or) where are the charges specified..in which file
>
> Any suggestions are appreciated...
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 8 Oct 2017 13:08:37 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding charges for atoms in a molecule
> Message-ID: <e9d15cec-04a2-2d12-7618-03fb9a1e21c9 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/8/17 1:04 PM, Dilip H N wrote:
> > Hello,
> > I have an amino-acid (eg. glycine) and water mixture, and by using
> charmm36
> > ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
> > abc.gro command.
> > 1] In the topology file, the charges for each atom are assigned. from
> where
> > are these charges assigned..?? is it from the .rtp file, itp file..??
>
> Charges are in the .rtp file (see the manual for how pdb2gmx works).
>
> > 2] If so, I compared the charges in the generated topology file and in
> the
> > merged.rtp file, but the charges are different in both the files...
>
> If you have just a single glycine, and you applied N- and C-terminal
> patches to it, the residue is modified according to the .n.tdb and
> .c.tdb entries. This is probably where the differences lie.
>
> > 3] I even checked in the ffnonbonded.itp file, but here for all the atom
> > types the charges are 0.00 only...(why is this so...??)
>
> Because those charges are never used for anything and have no meaning.
>
> > So, from where (or) where are the charges specified..in which file
>
> The "real" answer is that they are derived by those of us who work very
> hard to parametrize force fields, and you can get information on how
> that was done by reading the appropriate literature. This is really
> important to do so you understand how the force field works, pros and
> cons, etc. The implementation of charges into various files is just a
> technical detail.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 08 Oct 2017 18:06:51 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Equilibration using position restraints in
> NPT
> Message-ID:
> <CAMNuMAQmC5nDsJNLM26-Ai-=EoHZEU_PUrKzZmD=cqcacFD=Fw@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> The simplest explanation is that your box size is inappropriate for the
> contents. If the box wants to change size but the nanotube is restrained to
> fixed positions then you have an invalid model.
>
> Mark
>
> On Sun, 8 Oct 2017 15:39 Neha Gandhi <n.gandhiau at gmail.com> wrote:
>
> > This is a very common post on previous mailing list however, I am still
> not
> > able to fix the problem of position restraints during NPT.
> >
> > I have a carbon nanotube aligned to z-direction. I am trying to simulate
> > infinite nanotube using periodic conditions. It is common to use position
> > restraints for nanotube (most papers report this). I have imposed
> position
> > restraints on nanotube and in doing so, the coordinates fluctuates by
> 0.5-1
> > nm. This is not an issue with NVT simulation (Berendsen thermostat and
> > barostat). I tried different thermostats and barostats, they deform the
> > nanotube as previously discussed on gromacs mailing list.
> >
> > How do I equilibrate nanotube system with position restraints when used
> > together with pressure coupling? Should I play with the box size after
> > first NVT run?
> > The force field is opls based on gromacs guideline on CNTs and GROMACS
> > version is 5.1.4. The mdp parameters are below:
> >
> > Thank you in advance,
> >
> > Sincerely,
> > Neha
> >
> >
> >
> > title = OPLS Lysozyme NPT equilibration
> > define = -DPOSRES_CNT ; position restrain the protein
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 500000 ; 2
> > dt = 0.001 ; 2 fs
> > ; Output control
> > nstxout = 5000 ; save coordinates every 1.0 ps
> > nstvout = 5000 ; save velocities every 1.0 ps
> > nstenergy = 5000 ; save energies every 1.0 ps
> > nstlog = 5000 ; update log file every 1.0 ps
> > ;energygrps = Protein CNT Water NA
> > ; Bond parameters
> > continuation = yes ; Restarting after NVT
> > 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 = Berendsen ; modified Berendsen
> > thermostat
> > tc-grps = CNT Water ; two coupling groups - more accurate
> > tau_t = 0.2 0.2 ; time constant, in ps
> > ref_t = 310 310 ; reference temperature, one for
> > each group, in K
> > ; Pressure coupling is on
> > pcoupl = Berendsen ; Pressure coupling on in NPT
> > pcoupltype = isotropic ; uniform scaling of box
> > vectors
> > tau_p = 5.0 ; 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
> > periodic_molecules = yes
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = no ; Velocity generation is off
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 08 Oct 2017 18:06:51 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Equilibration using position restraints in
> NPT
> Message-ID:
> <CAMNuMAQmC5nDsJNLM26-Ai-=EoHZEU_PUrKzZmD=cqcacFD=Fw@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> The simplest explanation is that your box size is inappropriate for the
> contents. If the box wants to change size but the nanotube is restrained to
> fixed positions then you have an invalid model.
>
> Mark
>
> On Sun, 8 Oct 2017 15:39 Neha Gandhi <n.gandhiau at gmail.com> wrote:
>
> > This is a very common post on previous mailing list however, I am still
> not
> > able to fix the problem of position restraints during NPT.
> >
> > I have a carbon nanotube aligned to z-direction. I am trying to simulate
> > infinite nanotube using periodic conditions. It is common to use position
> > restraints for nanotube (most papers report this). I have imposed
> position
> > restraints on nanotube and in doing so, the coordinates fluctuates by
> 0.5-1
> > nm. This is not an issue with NVT simulation (Berendsen thermostat and
> > barostat). I tried different thermostats and barostats, they deform the
> > nanotube as previously discussed on gromacs mailing list.
> >
> > How do I equilibrate nanotube system with position restraints when used
> > together with pressure coupling? Should I play with the box size after
> > first NVT run?
> > The force field is opls based on gromacs guideline on CNTs and GROMACS
> > version is 5.1.4. The mdp parameters are below:
> >
> > Thank you in advance,
> >
> > Sincerely,
> > Neha
> >
> >
> >
> > title = OPLS Lysozyme NPT equilibration
> > define = -DPOSRES_CNT ; position restrain the protein
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 500000 ; 2
> > dt = 0.001 ; 2 fs
> > ; Output control
> > nstxout = 5000 ; save coordinates every 1.0 ps
> > nstvout = 5000 ; save velocities every 1.0 ps
> > nstenergy = 5000 ; save energies every 1.0 ps
> > nstlog = 5000 ; update log file every 1.0 ps
> > ;energygrps = Protein CNT Water NA
> > ; Bond parameters
> > continuation = yes ; Restarting after NVT
> > 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 = Berendsen ; modified Berendsen
> > thermostat
> > tc-grps = CNT Water ; two coupling groups - more accurate
> > tau_t = 0.2 0.2 ; time constant, in ps
> > ref_t = 310 310 ; reference temperature, one for
> > each group, in K
> > ; Pressure coupling is on
> > pcoupl = Berendsen ; Pressure coupling on in NPT
> > pcoupltype = isotropic ; uniform scaling of box
> > vectors
> > tau_p = 5.0 ; 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
> > periodic_molecules = yes
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = no ; Velocity generation is off
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 162, Issue 30
> ******************************************************
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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