[gmx-users] problem in energy minimization

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 12 20:54:04 CET 2009

Abhik Mukhopadhyay wrote:
> 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

When you created the topology, did pdb2gmx add a bond between the residues 
flanking the missing residues?  What was your pdb2gmx command line?

If you are sure that the missing residues will not influence the dynamics (think 
carefully!), then read in the manual about distance restraints.  If you have 
difficulties implementing these restraints, there are dozens of posts in the 
list archive that should guide you in how to use them.


> 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
> *Abhik Mukhopadhyay
> *
> Departamento Química / Faculdade de Ciências e Tecnologia
> Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
> Mob. 00351912991251
> http://xtal.dq.fct.unl.pt/
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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