On 11/14/18 5:28 AM, Gonzalez Fernandez, Cristina wrote:
Hi Justin,
I have taken a few days in answering you because I was trying to reduce the
discrepancies between the pressure I obtain after simulation and the one I set
in the .mdp file. However, I have no achieve very good results. As I indicated
in the previous email, in my simulations ref_p=1bar and ref_t=298K.
According to the output of gmx energy, the pressure average after the
simulation is 0.19bar , Err.est= 0.59 and RMSD=204,98; and for the temperature
average=298.003, Err.est=0,0032; RMSD=2,76.
From this results and your previous email, as the error (Err.est) in the
pressure is of the same magnitude as the
That error estimate is not relevant here. Your reported pressure is 0.19
± 205, which is indistinguishable from the target pressure of 1.
-Justin
pressure value after simulation, the pressure significantly differs from the
reference value (1bar), so for example, more simulation time will be required.
This is also supported by the high RMSD, which is in the order of hundreds. For
the temperature, the error is 5 orders of magnitude lower than the obtained
value and the RMSD is very low. This suggests that the system has reach the
equilibrium temperature. Are these reasons correct?
Another thing that makes me think that the pressure I obtain is not correct is
that the pressure I obtained after simulation and the one I obtain after
analysis also differ significantly (0.19 and 3.9 bar respectively).
I have used long both NPT equilibration and simulation times (50 ns) and the
results are similar to the ones I have indicated above, which apparently means
that the system is stable.
From these discrepancies, do you think the differences are not as important as
I am considering?, what could I do to obtain more accurate pressure values?
Regarding the Parrinello-Rahnman is "not stable for low pressures", I
understood that when using low pressures obtaining the reference pressure is sometimes
difficult by using Parrinello-Rahman. I was trying to use this article in order to
explain why my simulation pressures differ from the ref_p, but as you say, I have also
read papers that use Parrinello-Rahman for simulating 1bar systems.
Thank you very much for all your help,
C.
-----Mensaje original-----
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> En nombre de Justin Lemkul
Enviado el: jueves, 8 de noviembre de 2018 14:01
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] pcoupl Berendsen
On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote:
Dear Gromacs users,
In my simulations, I have specified ref_p= 1bar but after MD
simulation I obtain pressures equal to 0.19 bar (even
A pressure without an error bar is a meaningless value. The fluctuations of
pressure in most systems are on the order of tens or hundreds of bar, meaning
your result is indistinguishable from the target value.
with long simulation times) when using pcoupl=Parrinello-Rahman. I
know that Parrinello-Rahman is recommend for production runs and
Berendsen for NPT equilibration. However, I have read in an article
that Parrinello-Rahman is not stable for low pressures, so in such
situations its better to use Berendsen. I have tried to use Berendsen
for
I would be interested to know how this "not stable for low pressures"
was determined, because it seems completely unlikely to be true. Most MD
simulations nowadays use Parrinello-Rahman for pressure coupling at 1
bar/1 atm without any issue if the system is properly equilibrated (and if not,
the problem is with preparation, not the barostat itself).
MD simulation but I obtain this Warning and I cannot remove it with the
-maxwarn option.
"Using Berendsen pressure coupling invalidates the true ensemble for the
thermostat"
How can I use Berendsen for MD simulation?
Simply, you can't, and you shouldn't. The Berendsen method produces an invalid
statistical mechanical ensemble. It relaxes systems quickly and is therefore
still useful for equilibration, but should never be employed during data
collection. Full stop.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
