[gmx-users] Equilibration Problem.

[Dallas Warren]

Did you visualise the system? What would you expect the density of the
system to be?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 17 Sep 2019 at 19:17, Navneet Kumar Singh <navneetcdl at gmail.com>
wrote:

> 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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