[gmx-users] Logfile incorrectly (?) has dVbonded/dl terms

[David van der Spoel]

On 24/01/16 09:50, Dries Van Rompaey wrote:
> Hi gmx-users,
>
> I'm currently using FEP introduce a small change in my molecule. As a first
> step, I'm simply removing the coulomb interactions for the part that's
> being transformed into dummies. No other interactions are being modified.
>
> However, in my logfile I find:
> Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
> 9.44315e+01    1.50317e+02    1.02598e+02    5.65505e+00    7.01417e+01
> Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> -2.09477e+03    1.55917e+04   -5.21597e+02   -1.17294e+05    9.63595e+02
> Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
> -1.02932e+05    1.92182e+04   -8.37142e+04    2.99969e+02   -1.11454e+02
> Pressure (bar)       dEkin/dl      dVcoul/dl       dVvdw/dl    dVbonded/dl
> 8.26672e-01    0.00000e+00   -4.21612e+01    0.00000e+00    1.50215e+01
> dVrestraint/dl
> 0.00000e+00
>
> My lambda vectors are:
> mass_lambdas             = 0.00 0.00 0.00 0.00
> coul_lambdas             = 0.00 0.25 0.75 1.00
> vdw_lambdas              = 0.00 0.00 0.00 0.00
> bonded_lambdas           = 0.00 0.00 0.00 0.00
> restraint_lambdas        = 0.00 0.00 0.00 0.00
> temperature_lambdas      = 0.00 0.00 0.00 0.00
>
>
> I'm a bit confused by the dVbonded/dl in the logfile. Seeing as I'm not
> doing anything to my bonded interactions, shouldn't that be zero?
Most likely an exclusion correction but not sure.
>
> Thanks,
>
> Dries
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se