[gmx-users] (no subject)

[Mark Abraham]

On Mon, Nov 18, 2013 at 2:28 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> 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?
>

Use grompp -pp to see the results of how grompp interpreted all of your
inputs. There will be a position_restraints directive there somewhere, from
which you can work backwards to see its origin.

Mark



>
> Thanks in advance. I appreciate your suggestions.
>
>
>
> Sincerely,
> Shima
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