[gmx-users] Alanine dipeptide simulations

[Dallas Warren]

Is that really that surprising? 

 

You have variations of the order of 100s of bar and are looking for an
average that is 1.0

 

What you are observing is nothing out of the ordinary, from my
experience and what others have discussed here on the emailing list.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Sai Pooja
Sent: Wednesday, 8 September 2010 3:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Alanine dipeptide simulations

 

Hi

Yes, the fluctuations are large but even the average pressure hasn't
converged. Its close 2.5 bar. RMSD ~600 bar.

Pooja

On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren <Dallas.Warren at monash.edu>
wrote:

See http://www.gromacs.org/Documentation/Terminology/Pressure for
further details

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Dallas Warren
Sent: Wednesday, 8 September 2010 3:21 PM


To: Discussion list for GROMACS users

Subject: RE: [gmx-users] Alanine dipeptide simulations

 

What pressure has it reached?

 

Probably best graph the pressure versus time plot for the run and show
that.


I suspect what you are concerned about is the fact that with pressure
coupling, the pressure can fluctuation from step to step, very widely,
100s atm is not out of the question.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Sai Pooja
Sent: Wednesday, 8 September 2010 3:18 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Alanine dipeptide simulations

 

Hi,



I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator               = md
dt                       = 0.002
nsteps                   = 500000

; OUTPUT CONTROL OPTIONS
nstxout                  = 0                    ; No output, except for
last frame (coordinates)
nstvout                  = 0                    ; No output, except for
last frame (velocities)
nstfout                  = 0                    ; No output, except for
last frame (forces)
nstlog                   = 5000                ; Write every step to the
log
nstenergy                = 5000                    ; Write energies at
every step
xtc_grps                 = Protein SOL
nstxtcout                = 5000                    ; Do not write a
compressed trajectory
energygrps               = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = PME
fourierspacing           = 0.15
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                     = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no
; Temperature coupling
tcoupl                   = nose-hoover
tc-grps                  = Protein  Non-Protein
tau_t                    = 0.2      0.2
ref_t                    = 300      300

; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; OPTIONS FOR BONDS
constraints              = all-bonds


Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.


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