[gmx-users] Re: [gmx-developers] Re: long range interactions depend on bonds ?

[Michael Brunsteiner]

--- Berk Hess <gmx3 at hotmail.com> wrote:
> Hi Michael,
> 
> Do you use constraints?
> When constraints are present atoms might not be completely frozen,
> as they also need to satisfy the constraints.

well, I do use constraints (all bonds) but this does not seem to be the 
actual problem. I've got the output of two simulations, OLD and NEW.
md.mdp, conf.gro and index.ndx are identical in OLD and NEW,
ONLY difference: topol.top in OLD contains bond definitions between 
atoms in the frozen group A while topol.top in NEW does not (I double and 
triple checked that with diff) 

If I compare the content of the two md.log files I see that the 
only difference before the energy output starts is where the number
of constraints is reported, then the energies at step zero:

  OLD:
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    8.27019e+01    1.81476e+01    2.02982e+01   -1.49987e+01    1.19705e+04
   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.   Total Energy
   -7.81710e+04   -6.11122e+03   -7.22056e+04    1.26054e+04   -5.96002e+04
  NEW:
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    8.27019e+01    1.81476e+01    2.02982e+01   -1.49987e+01    1.19705e+04
   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.   Total Energy
   -7.81710e+04   -5.40009e+03   -7.14945e+04    1.11621e+04   -6.03324e+04

Mind that all energies are identical in A and B, ONLY the Coulomb (LR)
values differ considerably. Later the other energy terms also start to
differ somewhat (not surprisingly).
This must mean that the declaration of bonds does something
to the Coul-LR energy, why ?

groetjes,
Michael


additional info:
All the frozen atoms in my sims have a mass of 1.0e+12, resulting in 
identical positions of the frozen atoms in conf.gro and confout.gro. 
also are all bon-lengths in the frozen part at their equilibrium
values, therefore Lincs has no probelm with the frozen atoms when
bonds are defined.

the md.mdp:

title           = MD
cpp             = /usr/bin/cpp
;
integrator      = md
dt              = 0.002
nsteps          = 400000
;
comm_mode       =  linear
nstcomm         =  100
comm_grps       =  HOH
;
nstxtcout       =  100
xtc_grps        =  System
xtc_precision   =  1000.0
nstxout         =  0
nstvout         =  0
nstfout         =  0
nstlog          =  100
nstenergy       =  100
;
energygrps      = gpi ped HOH
freezegrps      = gpi
freezedim       = Y Y Y
energygrp_excl  = gpi gpi
;
nstlist         = 10
ns_type         = grid
pbc             = xyz
;
rlist           = 1.4
;
vdwtype         = shift
rvdw            = 1.2
rvdw_switch     = 0.0
DispCorr        = no
;
coulombtype     = PME
rcoulomb        = 1.2
fourierspacing  = 0.1
ewald_geometry  = 3d
;
tcoupl          = nose-hoover
tc_grps         = System
tau_t           = 0.1
ref_t           = 299.0
;
pcoupl           = no
;
constraints          = all-bonds
constraint_algorithm = lincs
unconstrained_start  = no
lincs_order          = 4
morse                = no
;
gen_vel              =  no




		
__________________________________
Do you Yahoo!?
Yahoo! Mail - Helps protect you from nasty viruses.
http://promotions.yahoo.com/new_mail