[gmx-users] Equilibration using position restraints in NPT
Alex
nedomacho at gmail.com
Sun Oct 8 23:36:25 CEST 2017
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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