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 <[email protected]> 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: [email protected] [mailto:
[email protected]] On Behalf Of Mark
Abraham
Sent: 17 October 2017 10:28
To: [email protected]
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 <[email protected]
wrote:
Is simulated annealing carried out during NPT or in the production run?
Akash
-----Original Message-----
From: [email protected] [mailto:
[email protected]] On Behalf Of Justin
Lemkul
Sent: 20 September 2017 03:20
To: [email protected]
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
--
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
303 Engel Hall
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[email protected] | (540) 231-3129
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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
[email protected] | (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
[email protected] | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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