[gmx-users] Equilibration Problem.

[Navneet Kumar Singh]

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.





*Energy                      Average   Err.Est.     RMSD
Tot-Drift-------------------------------------------------------------------------------Pressure
                  0.261272     0.49      49.1061        1.55678  (bar)*


*Density                            213.361       0.58       1.18799
       4.08348 (kg/m^3)*


*Temperature                       300.002       0.04      2.38265
-0.0854606  (K)*

*-------------------------------------------------------------------------------*

*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 <https://fil.email/ic2yZ4x3>)
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*


     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>

<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

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