[gmx-users] position restraint term

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Nov 18 15:30:43 CET 2013




Dear gmx users,


My simulated system contains is composed of lipid, protein and water molecules.
The NPT and NVT steps were done with position restraints on protein atoms. Then I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". But I still see the position restraint term in md.log file, however it seems to be small.

Forexample as below:


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    4.22077e+03    2.41766e+04    1.67865e+04    1.72538e+02   -1.02944e+01
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    2.65248e+03   -3.79682e+04    1.09363e+04   -1.49330e+03   -2.05391e+05
   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
   -9.97720e+02    4.84025e+01   -1.86867e+05    6.61349e+04   -1.20732e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12903e+02   -1.07476e+02    2.87101e+02    1.52447e-06

Would you please let me know what this term means? And why position restraints still exist? Is this amount of position restraint affects the results significantly? 


Thanks in advance. I appreciate your suggestions.



Sincerely,
Shima 


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