[gmx-users] Running MD simulations at a particular temperature
Dilip H N
cy16f01.dilip at nitk.edu.in
Wed Oct 18 15:42:00 CEST 2017
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
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 temperature,
>>> 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
>>>
>>> ==================================================
>>>
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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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> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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--
With Best Regards,
DILIP.H.N
Ph.D Student
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