Re: [gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure
On 11/1/14 11:56 PM, Agnivo Gosai wrote: Dear Users I am sharing a few plots through Google Drive. If you are able to view the files then kindly comment. My workflow is as follows :- 1) Topolgy preparation with AMBER99SB-Parmbsc0 ff in GROMACS 4.5.6. TIP3P water model. 2) Putting the complex in a box , using spc216 to solvate , adding ions. 3) Energy minimization with steepest descent. 4) 100 ps NVT equilibration with V-rescale thermostat. Ref T = 300 K , Avg. T = 299.7 K and Total Energy also remained constant. 5) 1st NPT simulation with Berendsen barostat (Ref. Pressure = 1 bar) having the following results : ( A)Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Pressure-5.57066.284.808538.1219 (bar) (B)All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Density 1012.13 0.551.871723.17412 (kg/m^3) 6) 2nd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : These are the average values :- Energy Average Err.Est. RMSD Tot-Drift -- Pressure -0.299523 0.64 93.313 -1.18081 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.32 0.261.685760.82485 (kg/m^3) 7)3rd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift - Pressure2.039590.995.9974 -6.788 (bar) All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.8 0.151.60294 0.243262 (kg/m^3) All the NPT equilibrations are of 100 ps and are continued from the previous equilibration. I observe that the average pressure has not yet reached the reference pressure and in the 3rd NPT run the Err.Est. , RMSD and Drift has increased. I have gone through the different comments and suggestions to my earlier posts. I am thinking of a 500 ps or 1 ns run with the Parinello Rahman barostat. Or am I failing to understand the physical significance of these average values and should have stopped after the 2nd NPT equilibration ? em_potential.png https://docs.google.com/file/d/0B-U8uULVZjfRZ0xfZGVrLVRYQVU/edit?usp=drive_web npt1_density.png https://docs.google.com/file/d/0B-U8uULVZjfRYUpKeGZfenNqRnM/edit?usp=drive_web npt1_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRa1FSWkNCTkxkM28/edit?usp=drive_web npt1_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRcmFmdHBybjZRTnM/edit?usp=drive_web npt2density.png https://docs.google.com/file/d/0B-U8uULVZjfRaUZKa1JJNWJCcU0/edit?usp=drive_web npt2_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRTng2eW1iQUxPamc/edit?usp=drive_web npt3_density.png https://docs.google.com/file/d/0B-U8uULVZjfRUGJSQU9MRnhlUTQ/edit?usp=drive_web npt3_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRcXFJZkt3N1YtdzQ/edit?usp=drive_web nvt_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRLTNNcmlEcFNSWDg/edit?usp=drive_web nvt_totalenergy.png https://docs.google.com/file/d/0B-U8uULVZjfRNFBZd05kMXNoYW8/edit?usp=drive_web Could anybody suggest why the reference pressure is not being reached ? Pressure is incredibly noisy, and you're going to get a distribution of values that varies wildly. Think generally about the statistics: if you were given three averages and standard deviations of -5.5 ± 85, -0.3 ± 93, and 2.0 ± 96, would you be able to say that they are significantly different from 1? Of course, you can do that analysis, but it's pretty clear that they're not. I have only seen an average pressure come out to 1.0 probably once so far in my career, though unfortunately (?) it is the case with one of my tutorials, so now everyone expects it to always happen :) Net result: your results are fine. Maybe over very long time periods you'll get to 1.0 or very close to it, but there is nothing wrong with your simulations and you're getting what you should be. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II,
Re: [gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure
Pressure is incredibly noisy, and you're going to get a distribution of values that varies wildly. Think generally about the statistics: if you were given three averages and standard deviations of -5.5 ± 85, -0.3 ± 93, and 2.0 ± 96, would you be able to say that they are significantly different from 1? That really depends on the number of statistically independent observations in the samples. Without those numbers, the question is pretty much meaningless from the point of view of statistics. In a simulation of 100 ps the number of uncorrelated frames is pretty low. Cheers, Tsjerk -- 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.
[gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure
Dear Users I am sharing a few plots through Google Drive. If you are able to view the files then kindly comment. My workflow is as follows :- 1) Topolgy preparation with AMBER99SB-Parmbsc0 ff in GROMACS 4.5.6. TIP3P water model. 2) Putting the complex in a box , using spc216 to solvate , adding ions. 3) Energy minimization with steepest descent. 4) 100 ps NVT equilibration with V-rescale thermostat. Ref T = 300 K , Avg. T = 299.7 K and Total Energy also remained constant. 5) 1st NPT simulation with Berendsen barostat (Ref. Pressure = 1 bar) having the following results : ( A)Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Pressure-5.57066.284.808538.1219 (bar) (B)All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Density 1012.13 0.551.871723.17412 (kg/m^3) 6) 2nd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : These are the average values :- Energy Average Err.Est. RMSD Tot-Drift -- Pressure -0.299523 0.64 93.313 -1.18081 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.32 0.261.685760.82485 (kg/m^3) 7)3rd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift - Pressure2.039590.995.9974 -6.788 (bar) All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.8 0.151.60294 0.243262 (kg/m^3) All the NPT equilibrations are of 100 ps and are continued from the previous equilibration. I observe that the average pressure has not yet reached the reference pressure and in the 3rd NPT run the Err.Est. , RMSD and Drift has increased. I have gone through the different comments and suggestions to my earlier posts. I am thinking of a 500 ps or 1 ns run with the Parinello Rahman barostat. Or am I failing to understand the physical significance of these average values and should have stopped after the 2nd NPT equilibration ? em_potential.png https://docs.google.com/file/d/0B-U8uULVZjfRZ0xfZGVrLVRYQVU/edit?usp=drive_web npt1_density.png https://docs.google.com/file/d/0B-U8uULVZjfRYUpKeGZfenNqRnM/edit?usp=drive_web npt1_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRa1FSWkNCTkxkM28/edit?usp=drive_web npt1_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRcmFmdHBybjZRTnM/edit?usp=drive_web npt2density.png https://docs.google.com/file/d/0B-U8uULVZjfRaUZKa1JJNWJCcU0/edit?usp=drive_web npt2_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRTng2eW1iQUxPamc/edit?usp=drive_web npt3_density.png https://docs.google.com/file/d/0B-U8uULVZjfRUGJSQU9MRnhlUTQ/edit?usp=drive_web npt3_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRcXFJZkt3N1YtdzQ/edit?usp=drive_web nvt_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRLTNNcmlEcFNSWDg/edit?usp=drive_web nvt_totalenergy.png https://docs.google.com/file/d/0B-U8uULVZjfRNFBZd05kMXNoYW8/edit?usp=drive_web Could anybody suggest why the reference pressure is not being reached ? Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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.
