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<p style="margin: 0px;">Nikhil,</p>
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<p style="margin: 0px;"><span>I had a similar problem, and was getting the same error. In my case the order of my atoms was different in my pdb/gro and my top/itp file. This made my system do a weird inversion, due to incorrect placement of atoms. And my energies were terrible.</span></p>
<p style="margin: 0px;"><span> </span></p>
<p style="margin: 0px;"><span>Hope this helps,</span></p>
<p style="margin: 0px;"><span>TJ Mustard<br />
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<br />
On December 28, 2010 at 8:26 AM nikhil damle <pdnikhil@yahoo.co.in> wrote:<br />
<br />
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Hi,<br />
I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent.<br />
<br />
System Details:<br />
# Atoms = 4488 (# Res = 582)<br />
octahedron box with d = 0.9<br />
Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 1048.86 g/L)<br />
<br />
System subjected to energy minimisation,<br />
Only warning arising during grompp:<br />
-------------------------------------------------------<br />
WARNING 1 [file dimer.top, line 46]:<br />
  86974 non-matching atom names<br />
  atom names from dimer.top will be used<br />
  atom names from neutral.pdb will be ignored<br />
-------------------------------------------------------<br />
This was neglected using -maxwarn option and contd...<br />
Error during minimisation run (mdrun):<br />
-------------------------------------------------------<br />
Steepest Descents:<br />
   Tolerance (Fmax)   =  1.00000e+03<br />
   Number of steps    =        50000<br />
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.04150e+23 Fmax=         inf, atom= 37<br />
Stepsize too small, or no change in energy.<br />
Converged to machine precision,<br />
but not to the requested precision Fmax < 1000<br />
<br />
Double precision normally gives you higher accuracy.<br />
<br />
writing lowest energy coordinates.<br />
<br />
Steepest Descents converged to machine precision in 15 steps,<br />
but did not reach the requested Fmax < 1000.<br />
Potential Energy  =  6.9065950e+23<br />
Maximum force     =            inf on atom 37<br />
Norm of force     =            inf<br />
-----------------------------------------------------<br />
<br />
1) I thought that the box size is too small so that dimer is not able to move at all and hence the energy is too high. But I am getting same error even if box size is increased to 2.0 nm<br />
2) I checked my initial structure and even the neutralised structure post solvation only to find that it is not broken. (My system has a missing loop which I have modeled using modeler9v8 and then subjected it to MD in solvent.)<br />
<br />
What could possibly go wrong ? Could it be really the step size or precision although I do not think so !<br />
<br />
Regards,<br />
Nikhil
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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