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> a...@imtech.res.in<br/> > <b>An:</b> gmx-users@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/> > ______________________________________________________________________<br/> > सूक्ष्मजीव > प्रौद्योगिकी > संस्थान > (वैज्ञानिक > औद्योगिक > अनुसंधान > परिषद)<br/> > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)<br/> > सैक्टर 39 ए, > चण्डीगढ़ / Sector 39-A, > Chandigarh<br/> > पिन कोड/PIN CODE :160036<br/> > दूरभाष/EPABX :0172 6665 201-202<br/> > --<br/> > gmx-users mailing list gmx-users@gromacs.org<br/> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"; > target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/> > * Please search the archive at <a > href="http://www.gromacs.org/Support/Mailing_Lists/Search"; > target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before > posting!<br/> > * Please don't post (un)subscribe requests to the list. Use the<br/> > www interface or send it to gmx-users-requ...@gromacs.org.<br/> > * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"; > target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></div> > </div> > </div> > </div></div></body></html> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ______________________________________________________________________ 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
