[gmx-users] g_dist problem in Implicit solvent

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 5/14/13 11:37 PM, Tong Li wrote:
> Hi Justin,
>
> Really appreciate your prompt reply! I got the inconsistence, the atom index in
> the original tpr file is different with the ones in xtc result file. However, I
> have no ideas what caused this… Some atoms are not in the ‘tpr’ file, but appear
> in the traj file (xtc) and also in the output geometry file (gro).
>

This is impossible.  If atoms are not in a .tpr file, they can't be written to 
configurations and trajectories.  Have you mixed up any of your files?  Use of 
gmxcheck and gmxdump will clarify what you have in what file.

-Justin

> I was using absolute implicit solvent simulation, never used any or deduct any
> water molecules from the simulation system. From geometry optimization, to nvt
> relaxation, then steered MD simulation in nvt assemble.
>
> Thanks a lot for your kind help!
>
> Cheers,
>
> Tong
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
>
> ; Method for doing electrostatics
>
> coulombtype              = cut-off
>
> rcoulomb                 = 1.2
>
> ; Relative dielectric constant for the medium and the reaction field
>
> epsilon_r                = 2
>
> epsilon_rf               = 0
>
> ; Method for doing Van der Waals
>
> vdw-type                 = cut-off
>
> ; cut-off lengths
>
> rvdw                     = 1.2
>
> ; Temperature coupling is on
>
> tcoupl                   = Berendsen      ; modified Berendsen thermostat
>
> tc-grps                  = Protein Non-Protein   ; two coupling groups - more
> accurate
>
> tau_t                     = 0.1      0.1          ; time constant, in ps
>
> ref_t                      = 310     310         ; reference temperature, one
> for each group, in K
>
> implicit-solvent = GBSA
>
> algorithm              = HCT
>
> rgbradii                  = 1.2
>
> ; pull code
>
> pull            = umbrella
>
> pull_geometry   = distance
>
> pull_dim        = Y Y Y
>
> pull_start      = yes
>
> pull_ngroups    = 1
>
> pull_group0     = non-Protein
>
> pull_group1     = Protein
>
> pull_init1      = 0
>
> pull_rate1      = -2
>
> pull_k1         = 2000      ; kJ mol^-1 nm^-2
>
> pull_nstxout    = 100      ; every 0.2 ps
>
> pull_nstfout    = 100      ; every 0.2 ps
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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