[gmx-users] energy minimization in charged systems

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Apr 8 07:22:53 CEST 2010

What are the atoms that are causing the problems actually doing, where are they located etc?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble a nail. 

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Ravi Bhadauria
Sent: Thursday, 8 April 2010 3:11 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] energy minimization in charged systems

Hi all,

I am trying to simulate a electroosmotic flow in a nanochannel. System consists of water + (Cl-) ions in a channel confined of silicon <111> walls. I start with taking water as only solvent, equilibrating the system for about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-) ions. Walls are charged appropriately to maintain electro-neutrality in the system. The problem is with Energy minimization after inserting ions using steep algorithm (haven't turned on the electric field yet). I am getting an error like this:

t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates


Steepest Descents converged to machine precision in 88 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.75456106043895e+06
Maximum force     =  1.07111309902475e+11 on atom 4898
Norm of force     =  1.48772609239112e+09

If it were only couple of such molecules, I could have removed them easily from the gro file. The problem is twofold, there are around 10 molecules which give this error message, plus even after removal of these molecules, energy minimization results in the same error on different sets of molecules. I have tried a number of ways to tackle this including tuning the time step. Is there any way to avoid this? Any help would be appreciated.

Thanks in advance.

Ravi Bhadauria

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