[gmx-users] Running MD simulations at a particular temperature

Justin Lemkul jalemkul at vt.edu
Wed Oct 18 15:43:25 CEST 2017



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 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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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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