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

Wed Oct 18 15:16:35 CEST 2017

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

==================================================