So, what should I aim for when running an NPT simulation?
Pooja
On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren <[email protected]
<mailto:[email protected]>> wrote:
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
[email protected] <mailto:[email protected]>
+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a nail.
*From:* [email protected]
<mailto:[email protected]>
[mailto:[email protected]
<mailto:[email protected]>] *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
<[email protected] <mailto:[email protected]>> 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
[email protected] <mailto:[email protected]>
+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a nail.
*From:* [email protected]
<mailto:[email protected]>
[mailto:[email protected]
<mailto:[email protected]>] *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
[email protected] <mailto:[email protected]>
+61 3 9909 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a nail.
*From:* [email protected]
<mailto:[email protected]>
[mailto:[email protected]
<mailto:[email protected]>] *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
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