Aw: [gmx-users] unable to equilibrate pressure in npt
amin at imtech.res.in
amin at imtech.res.in
Sat Jul 27 06:57:11 CEST 2013
Thanks for the explanation and the suggestions. The values I mentioned in the
last mail were obtained when using tau_p = 2. I have tried changing tau_p in the
mdp file to 0.8 and 1.0. With tau_p = 1.0 the average pressure is around 0.9 but
with tau_p = 0.8 the pressure is ~ -0.3 (time = 10ns). Is there something else I
might be doing wrong? To add more information, I am using the same mdp file as
given in the lysozyme tutorial except using amber03 ILDN and changing the
barostat as I mentioned. Should I try increasing the coupling time to more than
2 ? Any suggestions would be highly appreciated.
Amin
I did such things in the past, and had similar issues. First of,
> somone may have beter suggestions. The coupling time will bring it down a
> bit in the .mdp file (0.2 Vs 2 picoseconds. However, I have found that you
> will still see large fluctuations around a mean once equilibrated which can vary
> by 10 to 60, 70 Atomospheres depending on the pressure coupling algorythim
> used. If it oscillates around this mean, without large up or down changes
> I assume it is eq'd. Basically, if you look at it from the perspective
> of what pressure itself entails, it is the direct kenetic force of small
> molecules bumping into each other, so a simple protein movmeent in a small unit
> cell is turned by the computer into a molar ration, which looks crazy at the
> macroscopic level, but in reality you do not usually have the unit cell in such
> a deminsion. This is of course unless your system is made of nothing other
> than small molecules, which take off a 0 to the oscillation range. the
> pressure algorythms just keep it from going to insanly large limits, such as an
> ice cube because of 200 kcal/mol - enthalpy or boiling in the reverse, by
> pretending there is a universal pressure applied to the unit cell...so a
> generalized correction for the fact that the unit cell is not really
> representing infinaty as it is treated by the computer...based on real
> macroscopic pressures. I may be wrong , but this is my assumption.</div>
>
> <div> </div>
>
> <div>Stephan Watkins</div>
>
> <div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px;
> border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space;
> -webkit-line-break: after-white-space;">
> <div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 25. Juli 2013
> um 18:22 Uhr<br/>
> <b>Von:</b> amin at imtech.res.in<br/>
> <b>An:</b> gmx-users at gromacs.org<br/>
> <b>Betreff:</b> [gmx-users] unable to equilibrate pressure in npt</div>
>
> <div name="quoted-content">Dear gromacs users,<br/>
> I know similar issues have been raised many times on the list but I am unable
> to<br/>
> solve the problem so I am seeking your advice. I am trying to simulate a
> protein<br/>
> in a dodecahedron box. The system size is ~30k atoms. I have followed the<br/>
> methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and<br/>
> production. However the average pressure values after 5, 10, 20 ns of npt<br/>
> equilibration are not coming close to the reference pressure i.e 1 bar when<br/>
> using parrinello rahman. I checked the mailing list and tried using
> Berendson<br/>
> and after 10 ns I get average pressure close to 1 (0.85). However when I
> switch<br/>
> to parrinello rahman for production run the average pressure again goes far
> from<br/>
> 1. Can someone please help me with this? Here are the g_energy outputs from<br/>
> equilibration (parrinello rahman, 20ns) and production run (10ns after<br/>
> Berendson).<br/>
> <br/>
> Pressure 0.0300644 0.38 134.243 1.57106 (bar)<br/>
> <br/>
> Pressure -0.0405509 0.79 134.204 0.151638 (bar)<br/>
> <br/>
> Can someone please help me with this?<br/>
> <br/>
> Regards.<br/>
> Amin.<br/>
> <br/>
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______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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