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

Justin Lemkul jalemkul at vt.edu
Wed Oct 25 15:35:17 CEST 2017



On 10/25/17 9:33 AM, Dilip H N wrote:
> 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..??

Read the literature. You shouldn't be using a force field if you don't 
know how it works, what it's good for and what it fails at, and what the 
best practices are.

-Justin

> 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
>>>
>>>
>>> <https://mailtrack.io/> Sent with Mailtrack
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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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>>>> Gromacs Users mailing list
>>>>
>>>> * 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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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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