[gmx-users] problem in energy minimization

Abhik Mukhopadhyay abhikuohyd at yahoo.com
Thu Mar 12 20:31:59 CET 2009

Hi everyone, 
I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization with all-bonds constraint, but that i guess did not do it properly. 
This is the last part of the minimization run 

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1#

Back Off! I just backed up ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.2785961e+05
Maximum force     =  5.1547680e+08 on atom 1004
Norm of force     =  8.2600877e+08

My question is how can I run a simulation on these structure keeping that part as it is?

Thanking you in advance.


Abhik Mukhopadhyay
  Departamento Química / Faculdade de Ciências e Tecnologia 
 Universidade Nova de Lisboa , 2829-516 Caparica, Portugal 

Mob. 00351912991251

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