So, what should I aim for when running an NPT simulation?<br><br>Pooja<br><br><div class="gmail_quote">On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Is that really that surprising? </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">You have variations of the order of 100s of bar and are looking
for an average that is 1.0</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">What you are observing is nothing out of the ordinary, from my
experience and what others have discussed here on the emailing list.</span></p><div class="im">
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">+61 3 9909 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div><div style="border-width: medium medium medium 1.5pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; padding: 0cm 0cm 0cm 4pt;">
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<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On
Behalf Of </b>Sai Pooja<br>
<b>Sent:</b> Wednesday, 8 September 2010 3:38 PM<div class="im"><br>
<b>To:</b> Discussion list for GROMACS users<br>
</div><b>Subject:</b> Re: [gmx-users] Alanine dipeptide simulations</span></p>
</div>
</div><div><div></div><div class="h5">
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom: 12pt;">Hi<br>
<br>
Yes, the fluctuations are large but even the average pressure hasn't converged.
Its close 2.5 bar. RMSD ~600 bar.<br>
<br>
Pooja</p>
<div>
<p class="MsoNormal">On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>> wrote:</p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">See <a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a>
for further details</span></p>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical
Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">+61 3 9909 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div>
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<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Dallas Warren<br>
<b>Sent:</b> Wednesday, 8 September 2010 3:21 PM</span></p>
<div>
<p class="MsoNormal"><span style="font-size: 10pt;"><br>
<b>To:</b> Discussion list for GROMACS users</span></p>
</div>
<p class="MsoNormal"><b><span style="font-size: 10pt;">Subject:</span></b><span style="font-size: 10pt;"> RE: [gmx-users] Alanine dipeptide simulations</span></p>
</div>
</div>
<div>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">What pressure has it reached?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Probably best graph the pressure versus
time plot for the run and show that.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"><br>
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.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical
Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">+61 3 9909 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div>
<div style="border-width: medium medium medium 1.5pt; border-style: none none none solid; padding: 0cm 0cm 0cm 4pt; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue;">
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<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>Sai Pooja<br>
<b>Sent:</b> Wednesday, 8 September 2010 3:18 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Alanine dipeptide simulations</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal">Hi,</p>
<div>
<div>
<p class="MsoNormal"><br>
<br>
I am running an npt simulation on alanine dipeptide in explicit solvent using
charmm forcefield and tip3p.<br>
<br>
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.<br>
<br>
I don;t understand why is this the case.<br>
<br>
My mdp file:<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator
= md<br>
dt
= 0.002<br>
nsteps
= 500000<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout
= 0
; No output, except for last frame (coordinates)<br>
nstvout
=
0
; No output, except for last frame (velocities)<br>
nstfout
=
0
; No output, except for last frame (forces)<br>
nstlog
=
5000
; Write every step to the log<br>
nstenergy
=
5000
; Write energies at every step<br>
xtc_grps
= Protein SOL<br>
nstxtcout
=
5000
; Do not write a compressed trajectory<br>
energygrps
= Protein SOL ; Write energy information separately for these groups<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist
= 5<br>
ns-type
= Grid<br>
pbc
= xyz<br>
rlist
= 0.9<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype
= PME<br>
fourierspacing =
0.15<br>
rcoulomb
= 0.9<br>
vdw-type
= Cut-off<br>
rvdw
= 1.0<br>
<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx
= 0<br>
fourier_ny
= 0<br>
fourier_nz
= 0<br>
; EWALD/PME/PPPM parameters =<br>
pme_order
= 4<br>
ewald_rtol
= 1e-05<br>
epsilon_surface = 0<br>
optimize_fft
= no<br>
; Temperature coupling<br>
tcoupl
= nose-hoover<br>
tc-grps
= Protein Non-Protein<br>
tau_t
= 0.2 0.2<br>
ref_t
= 300 300<br>
<br>
; Pressure coupling<br>
Pcoupl
= Parrinello-Rahman<br>
Pcoupltype
= Isotropic<br>
tau_p
= 1.0<br>
compressibility = 4.5e-5<br>
ref_p
= 1.0<br>
<br>
; OPTIONS FOR BONDS<br>
constraints
= all-bonds<br>
<br>
<br>
Pooja<br>
<br>
<br>
<br clear="all">
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.</p>
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