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

[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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] System reaches ~124K after simulated
>          annealing upto 300K
> Message-ID: <8fe97070-c577-de07-ba25-64a7230f645b at 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                   = 50000 ; 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                    = 0.1        0.1        ; Coupling time constant,
>> controlling strength of coupling
>> ref_t                    = 300        300    ; 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
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> 
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> End of gromacs.org_gmx-users Digest, Vol 158, Issue 106
> *******************************************************
> 

-- 
==================================================

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

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

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