Re: Aw: [gmx-users] unable to equilibrate pressure in npt
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. > > > > Stephan Watkins > > > Gesendet: Donnerstag, 25. Juli > 2013 > um 18:22 Uhr > Von: a...@imtech.res.in > An: gmx-users@gromacs.org > Betreff: [gmx-users] unable to equilibrate pressure in npt > > Dear gromacs users, > I know similar issues have been raised many times on the list but I am unable > to > solve the problem so I am seeking your advice. I am trying to simulate a > protein > in a dodecahedron box. The system size is ~30k atoms. I have followed the > methodology given in the lysozyme tutorial i.e. minimization, nvt, npt > and > production. However the average pressure values after 5, 10, 20 ns of npt > equilibration are not coming close to the reference pressure i.e 1 bar > when > using parrinello rahman. I checked the mailing list and tried using > Berendson > and after 10 ns I get average pressure close to 1 (0.85). However when I > switch > to parrinello rahman for production run the average pressure again goes far > from > 1. Can someone please help me with this? Here are the g_energy outputs > from > equilibration (parrinello rahman, 20ns) and production run (10ns after > Berendson). > > Pressure 0.0300644 0.38 134.243 1.57106 (bar) > > Pressure -0.0405509 0.79 134.204 0.151638 (bar) > > Can someone please help me with this? > > Regards. > Amin. > > __ > 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"; > target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at href="http://www.gromacs.org/Support/Mailing_Lists/Search"; > target="_blank">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"; > target="_blank">http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing listgmx-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)subscri
Aw: [gmx-users] unable to equilibrate pressure in npt
Dear 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. Stephan Watkins Gesendet: Donnerstag, 25. Juli 2013 um 18:22 Uhr Von: a...@imtech.res.in An: gmx-users@gromacs.org Betreff: [gmx-users] unable to equilibrate pressure in npt Dear gromacs users, I know similar issues have been raised many times on the list but I am unable to solve the problem so I am seeking your advice. I am trying to simulate a protein in a dodecahedron box. The system size is ~30k atoms. I have followed the methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and production. However the average pressure values after 5, 10, 20 ns of npt equilibration are not coming close to the reference pressure i.e 1 bar when using parrinello rahman. I checked the mailing list and tried using Berendson and after 10 ns I get average pressure close to 1 (0.85). However when I switch to parrinello rahman for production run the average pressure again goes far from 1. Can someone please help me with this? Here are the g_energy outputs from equilibration (parrinello rahman, 20ns) and production run (10ns after Berendson). Pressure 0.0300644 0.38 134.243 1.57106 (bar) Pressure -0.0405509 0.79 134.204 0.151638 (bar) Can someone please help me with this? Regards. Amin. __ 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 -- gmx-users mailing listgmx-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
[gmx-users] unable to equilibrate pressure in npt
Dear gromacs users, I know similar issues have been raised many times on the list but I am unable to solve the problem so I am seeking your advice. I am trying to simulate a protein in a dodecahedron box. The system size is ~30k atoms. I have followed the methodology given in the lysozyme tutorial i.e. minimization, nvt, npt and production. However the average pressure values after 5, 10, 20 ns of npt equilibration are not coming close to the reference pressure i.e 1 bar when using parrinello rahman. I checked the mailing list and tried using Berendson and after 10 ns I get average pressure close to 1 (0.85). However when I switch to parrinello rahman for production run the average pressure again goes far from 1. Can someone please help me with this? Here are the g_energy outputs from equilibration (parrinello rahman, 20ns) and production run (10ns after Berendson). Pressure 0.0300644 0.38134.2431.57106 (bar) Pressure -0.0405509 0.79134.204 0.151638 (bar) Can someone please help me with this? Regards. Amin. __ 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 listgmx-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
