[gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure

[Agnivo Gosai]

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 [ 0.0000 through 100.0000 ps ], 1 data sets
All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------
Pressure                    -5.5706        6.2    84.8085    38.1219  (bar)
(B)All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------
Density                     1012.13       0.55    1.87172    3.17412
(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       0.26    1.68576    0.82485
(kg/m^3)
7)3rd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1
bar) having the following results :
Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets
All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------
Pressure                    2.03959        0.9    95.9974     -6.788  (bar)

All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------------------------------------
-------------------
Density                      1012.8       0.15    1.60294   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.