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

[Pandya, Akash]

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.

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)
; 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
> send a mail to gmx-users-request at gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.