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
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
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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
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