Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

2017-06-17 Thread Justin Lemkul 



On 6/17/17 2:23 AM, Apramita Chand wrote:

Dear Justin,
The normal (non-annealing) equilibration works fine. 100ps of NVT and it
easily reaches 300K. There are no error messages.
Am I doing the simulated annealing correctly?



Looks fine, other than generating velocities at 300 K but specifying 0 K as the 
initial temperature for annealing.  If you're just equilibrating a system, I 
think annealing is a waste of time.


-Justin


yours sincerely
Apramita

Message: 4
Date: Fri, 16 Jun 2017 13:21:18 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] System reaches ~124K after simulated
 annealing upto 300K
Message-ID: <8fe97070-c577-de07-ba25-64a7230f6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/16/17 10:38 AM, Apramita Chand wrote:

Dear All,
I have used the following nvt.mdp file to gradually warm my system upto
300K but just reach upto 124K. I have used variety of options in the
simulated annealing like taking less no. of time intervals but in vain
Then, I have to perform manually the gradual heating process which takes

me

to 300K
Why doesn't this work?



Anything that goes that haywire is simply unstable.  De-complicate your
life and
try to do a normal (non-annealing) MD and see if it works.  If not, then
diagnose further.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_
Unstable_System

-Justin


Yours sincerely,
Apramita



   VARIOUS PREPROCESSING OPTIONS
define   = -DPOSRES
; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002 ; time step (in ps)
nsteps   = 5 ; number of steps
; OUTPUT CONTROL OPTIONS
nstxout = 500   ; save coordinates every ps
nstvout = 500   ; save velocities every ps
nstenergy   = 500   ; save energies every ps
nstlog  = 500   ; update log file every ps
energygrps  = Protein SOL
; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME  ; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing   = 0.16 ; grid spacing for FFT
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
5
tcoupl   = v-rescale; Couple temperature to
external heat bath according to velocity re-scale method
tc-grps  =  Protein  SOL ; Use separate heat baths for
Protein and Non-Protein groups
tau_t= 0.10.1; Coupling time constant,
controlling strength of coupling
ref_t= 300300; Temperature of heat bath
; Dispersion correction
DispCorr = EnerPres ; account for vdw cut-off
; Pressure coupling is off
pcoupl  = no; no pressure coupling in
NVT
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes; Assign velocities to particles by
taking
them randomly from a Maxwell distribution
Different numbers give different sets of velocities
gen_temp = 300; Temperature to generate corresponding
Maxwell distribution
gen_seed = -1 ; Seed for (semi) random number
generation.
; OPTIONS FOR BONDS
constraints  = all-bonds ; All bonds will be treated as
constraints (fixed length)
continuation = no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
lincs_iter   = 1; accuracy of LINCS
lincs_order  = 4; also related to accuracy
; Simulated Annealing
annealing= single single
annealing_npoints= 4 4
annealing_time= 0 50 75 100 0 50 75 100
annealing_temp= 0 100 200 300 0 100 200 300



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


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==

Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

2017-06-17 Thread Apramita Chand 
Dear Justin,
The normal (non-annealing) equilibration works fine. 100ps of NVT and it
easily reaches 300K. There are no error messages.
Am I doing the simulated annealing correctly?

yours sincerely
Apramita

Message: 4
Date: Fri, 16 Jun 2017 13:21:18 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] System reaches ~124K after simulated
annealing upto 300K
Message-ID: <8fe97070-c577-de07-ba25-64a7230f6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/16/17 10:38 AM, Apramita Chand wrote:
> Dear All,
> I have used the following nvt.mdp file to gradually warm my system upto
> 300K but just reach upto 124K. I have used variety of options in the
> simulated annealing like taking less no. of time intervals but in vain
> Then, I have to perform manually the gradual heating process which takes
me
> to 300K
> Why doesn't this work?
>

Anything that goes that haywire is simply unstable.  De-complicate your
life and
try to do a normal (non-annealing) MD and see if it works.  If not, then
diagnose further.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_
Unstable_System

-Justin

> Yours sincerely,
> Apramita
>
>
>
>   VARIOUS PREPROCESSING OPTIONS
> define   = -DPOSRES
> ; RUN CONTROL PARAMETERS
> integrator   = md
> dt   = 0.002 ; time step (in ps)
> nsteps   = 5 ; number of steps
> ; OUTPUT CONTROL OPTIONS
> nstxout = 500   ; save coordinates every ps
> nstvout = 500   ; save velocities every ps
> nstenergy   = 500   ; save energies every ps
> nstlog  = 500   ; update log file every ps
> energygrps  = Protein SOL
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 0.9
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME  ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing   = 0.16 ; grid spacing for FFT
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 1.4
> ; Temperature coupling
> 5
> tcoupl   = v-rescale; Couple temperature to
> external heat bath according to velocity re-scale method
> tc-grps  =  Protein  SOL ; Use separate heat baths for
> Protein and Non-Protein groups
> tau_t= 0.10.1; Coupling time constant,
> controlling strength of coupling
> ref_t= 300300; Temperature of heat bath
> ; Dispersion correction
> DispCorr = EnerPres ; account for vdw cut-off
> ; Pressure coupling is off
> pcoupl  = no; no pressure coupling in
> NVT
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel  = yes; Assign velocities to particles by
> taking
> them randomly from a Maxwell distribution
> Different numbers give different sets of velocities
> gen_temp = 300; Temperature to generate corresponding
> Maxwell distribution
> gen_seed = -1 ; Seed for (semi) random number
> generation.
> ; OPTIONS FOR BONDS
> constraints  = all-bonds ; All bonds will be treated as
> constraints (fixed length)
> continuation = no   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> lincs_iter   = 1; accuracy of LINCS
> lincs_order  = 4; also related to accuracy
> ; Simulated Annealing
> annealing= single single
> annealing_npoints= 4 4
> annealing_time= 0 50 75 100 0 50 75 100
> annealing_temp= 0 100 200 300 0 100 200 300
>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


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