[gmx-users] Question about HREMD in .log file

[andrew ritchie]

So I've added :
---
couple-moltype           = Protein
couple-intramol          = yes
---
and now I have non-zero dVcoul/dl, but the dVvdw/dl terms are still zero.
 Why is this still zero/should I be concerned about that?
I'm also happy to no longer be seeing a 100% exchange rate (which I
previously forgot to mention was another reason this caught my attention).

---- run_hremd.N.mdp ----
integrator               = sd
tinit                    = 0
dt                       = 0.002
nsteps                   = 1000000 ; 500000 steps/ns

nstxout                  = 0
nstvout                  = 0
nstfout                  = 2500
nstlog                   = 500
nstenergy                = 500
nstdhdl                  = 100
nstcalcenergy            = 50
nstxtcout                = 2500 ; 500 steps/ps
xtc-precision            = 1000

cutoff-scheme            = Verlet
nstlist                  = 10
nstcalclr                = 1
ns_type                  = grid
pbc                      = xyz

coulombtype              = pme
rcoulomb                 = 0.9
fourierspacing           = 0.12
pme_order                = 4
epsilon-r                = 78
vdw-type                 = cut-off
rvdw-switch              = 0.7
rvdw                     = 0.9

constraints              = all-bonds
constraint_algorithm     = lincs

gen-vel                  = yes
gen-temp                 = 300
gen-seed                 = 47

ref_t                    = 300
tau_t                    = 2.00 ; every 2 ps, as suggested when sd used as
thermostat
tc_grps                  = system

free-energy              = yes
sc-alpha                 = 0.5
sc-power                 = 1
sc-r-power               = 6
calc-lambda-neighbors    = 1
init-lambda-state        = N
vdw-lambdas              = 0.0 0.0 0.0 0.0 0.1 0.2 0.5 1.0
coul-lambdas             = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0
couple-lambda0           = vdw-q ; all interactions are on at lambda=0
couple-lambda1           = none ; all interaction off at lambda=1
couple-moltype           = Protein
couple-intramol          = yes
----


On Thu, Aug 29, 2013 at 10:55 PM, drew.w.ritchie
<drew.w.ritchie at gmail.com>wrote:

> Greetings,
>
> I'm trying to use HREMD on a protein (100 residues) in water to better
> sample side chain conformational space in the canonical ensemble. The free
> energy part in my 8 .mdp files, with N ranging from 0 to 7, is :
>
> ---
> free-energy = yes
> nstdhdl = 100
> init-lambda-state = N
> coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0
> vdw-lambdas = 0.0 0.0 0.0 0.0 0.1 0.2 0.5 1.0
> sc-alpha = 0.5
> sc-r-power = 6
> couple-lambda0 = vdw-q
> couple-lambda1 = none
> ---
>
> My concern is in all of the .log files, I see something like this :
> ---
>            Step           Time         Lambda
>            2000        4.00000        0.00000
>
>    Energies (kJ/mol)
>           Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     3.07685e+03    4.19165e+03    1.55122e+02    1.74570e+03    2.55986e+02
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>    -2.92999e+04   -1.49852e+03    9.25653e+02   -2.04475e+04    1.13608e+05
>    Total Energy    Temperature Pressure (bar)      dVcoul/dl       dVvdw/dl
>     9.31607e+04    3.02344e+02    2.36558e+03    0.00000e+00    0.00000e+00
>    Constr. rmsd  Constr.2 rmsd
>     2.57681e-05    1.11671e-05
>
> Replica exchange at step 2000 time 4
>
> Accepted Exchanges:   0 7 5 6 2 3 1 4
> Order After Exchange: 5 2 0 6 7 4 3 1
> ---
>
> All of the Lambdas are 0 for all of the replicates and all of the dVcoul/dl
> and dVvdw/dl are also zero.  Does this mean all of my replicates have all
> interactions turned on?  If so, is it obvious where my mistake is based on
> the mdp snippet I've included?
>
> Thanks,
> Andrew Ritchie
>
>
>
>
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-- 
-Andrew Ritchie