[gmx-users] Running MD simulations at a particular temperature
Dilip H N
cy16f01.dilip at nitk.edu.in
Wed Oct 25 15:33:46 CEST 2017
Sir,
As u have mentioned in the link http://www.gromacs.org/Documen
tation/Terminology/Force_Fields/CHARMM the cutoffs are described here for
CHARMM FF.
So similarly, how can i get the cutoffs for OPLSAA, Amber, GROMOS etc.,
forcefields in gromacs..?? Is there any source, or only through literature
survey the cutoffs need to be fixed..??
Thank you..
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<#>
On Wed, Oct 18, 2017 at 7:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/18/17 9:41 AM, Dilip H N wrote:
>
>> Justin Sir,
>> Even i am also using Charmm 36FF. So as u have mentioned in previois
>> message, can u kindly suggest then what ate the correct cutoffs..??
>> And what would be the other modifications that needs to be done in order
>> to
>> incorporate the Charmm FF
>>
>
> I think I post this link to the mailing list weekly...
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
> Thank you
>>
>>
>>
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>>
>> On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 10/18/17 9:14 AM, Pandya, Akash wrote:
>>>
>>> So I equilibrated my system at 338.15 K , do I still need to use the
>>>> simulated annealing option to maintain that temperature? My NPT mdp
>>>> file is
>>>> shown below.
>>>>
>>>> Simply maintaining a temperature is done by employing a thermostat and
>>> reference temperature. Annealing is used to change temperature over time,
>>> so you don't need that here.
>>>
>>> title = CHARMM27 A33FabGLY NPT equilibration
>>>
>>>> define = -DPOSRES ; position restrain the protein
>>>> ; Run parameters
>>>> integrator = md ; leap-frog integrator
>>>> nsteps = 50000 ; 2 * 50000 = 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 = 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
>>>> ns_type = grid ; search neighboring grid cells
>>>> nstlist = 5 ; 10 fs
>>>> rlist = 1.0 ; short-range neighborlist cutoff (in
>>>> nm)
>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in
>>>> nm)
>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in
>>>> nm)
>>>>
>>>> Your title says CHARMM, but these aren't the correct cutoffs for using
>>> the
>>> CHARMM force field.
>>>
>>> -Justin
>>>
>>>
>>> ; 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 = Nose-Hoover ; Nose-Hoover thermostat
>>>> tc-grps = Protein Non-Protein ; two coupling groups - more
>>>> accurate
>>>> tau_t = 0.5 0.5 ; time constant, in ps
>>>> ref_t = 338.15 338.15 ; 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
>>>> refcoord_scaling = com
>>>> ; 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
>>>>
>>>>
>>>> Akash
>>>> -----Original Message-----
>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
>>>> Abraham
>>>> Sent: 17 October 2017 10:28
>>>> To: gmx-users at gromacs.org
>>>> Subject: Re: [gmx-users] Running MD simulations at a particular
>>>> temperature
>>>>
>>>> Hi,
>>>>
>>>> That's your question as part of your experimental design. Why do you
>>>> want
>>>> to do simulated annealing?
>>>>
>>>> Mark
>>>>
>>>> On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <
>>>> akash.pandya.15 at ucl.ac.uk
>>>> wrote:
>>>>
>>>> Is simulated annealing carried out during NPT or in the production run?
>>>>
>>>>> Akash
>>>>>
>>>>> -----Original Message-----
>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
>>>>> Lemkul
>>>>> Sent: 20 September 2017 03:20
>>>>> To: gmx-users at gromacs.org
>>>>> Subject: Re: [gmx-users] Running MD simulations at a particular
>>>>> temperature
>>>>>
>>>>>
>>>>>
>>>>> On 9/19/17 4:25 PM, Pandya, Akash wrote:
>>>>>
>>>>> Hi all,
>>>>>>
>>>>>> I want to run my MD simulation at 65 degrees Celsius. The mdp file
>>>>>> has a
>>>>>>
>>>>>> field as shown below:
>>>>>
>>>>> ref_t = 338.15 338.15 ; reference
>>>>>>
>>>>>> temperature, one for each group, in K
>>>>>
>>>>> I am wondering whether the simulation has already reached the
>>>>>> desired
>>>>>>
>>>>>> temperature or does it heat up to 65 degrees throughout the course of
>>>>> the simulation? I hope this makes sense.
>>>>>
>>>>> The answer depends on what you're doing. If you've set "gen-vel = yes"
>>>>> and "gen-temp = 338.15" then you are initializing a simulation with
>>>>> random velocities according to a Maxwell distribution at that
>>>>> temperature. If your system is at some other temperature and you're
>>>>> just trying to use a thermostat to force a change in that t
>>>>> <https://maps.google.com/?q=a+thermostat+to+force+a+change+in+that+t&entry=gmail&source=g>
>>>>> emperature,
>>>>> there's no real "warming"
>>>>> going on, rather the thermostat is going to push the velocity
>>>>> distribution towards the desired temperature. Warming a system is
>>>>> done via simulated annealing options.
>>>>>
>>>>> -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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>> --
>>>> Gromacs Users mailing list
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>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>>
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>>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>
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--
With Best Regards,
DILIP.H.N
Ph.D Student
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