[gmx-users] (no subject)

[Shima Arasteh]

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