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 <[email protected]> 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
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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 t
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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.
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
[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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==================================================
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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