[gmx-users] Equilibration using position restraints in NPT
Alex
nedomacho at gmail.com
Sun Oct 8 23:38:54 CEST 2017
In addition, the CNT edges have to be periodically commensurate.
On 10/8/2017 3:36 PM, Alex wrote:
> PBC for crystals are not set this way, this is why the simulator is
> turning the CNT into a pogo stick.
>
> Prior to any simulations, please calculate the correct PBC-compatible
> axial length using crystallographic considerations and CNT chirality,
> -box properly, generate topology with PBC, then proceed with EM, etc.
>
> Alex
>
>
> On 10/8/2017 3:29 PM, Neha Gandhi wrote:
>> 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
>>> ******************************************************
>>>
>>
>>
>
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