[gmx-users] grompp warning with SHAKE, but ok with LINCS

[Tsjerk Wassenaar]

Hi D_Roy,

The warning message is quite self-explanatory. Do read beyond the word
WARNING. As for the other question, the constraint algorithm stands apart
from the forcefield, unlike many other options. You can safely use Lincs
with G536.

Cheers,

Tsjerk

On Mar 17, 2012 10:31 AM, "D_Roy" <r.dipankar at gmail.com> wrote:

I trying to do an NVT simulation of a peptide in water with the following
mdp
parameters:

====
title           =      GROMOS53A6 NVT equilibration
define  =  -DPOSRES     ; position restrain the protein

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps  = 50000         ; 2 * 50000 = 100 ps
dt              = 0.002         ; 2 fs

; Output control
nstxout = 100           ; save coordinates every 0.2 ps
nstvout = 100           ; save velocities every 0.2 ps
nstxtcout       = 100           ; save coordinates to trajectory every 0.2
ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog  = 100           ; update log file every 0.2 ps

; Bond parameters
continuation    = no            ; first dynamics run

;bond constraint
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
constraint_algorithm = SHAKE    ;
shake_tol       = 0.0001        ; relative tolerance

; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5             ; 10 fs
rlist           = 0.8           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.4           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.4           ; short-range van der Waals cutoff (in nm)

; Electrostatics and ven der Waals
coulombtype   = Reaction-Field ; reaction-field for long-range
electrostatics
vdw-type        = Cut-off        ; van der Waals treatment for long-range
electrostatics
epsilon_rf           = 62                ; dielectric constant/relative
permitivitty

; Temperature coupling is on
tcoupl           = V-rescale            ; 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                    = 300  300             ; reference temperature,
one for each group, in
K

; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT

; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC

; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme

; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed

==========
When I run grompp with the command:

 grompp -v -f pr.mdp -c protein_mod1_EM_solv.gro -p protein_mod1.top -o
protein_mod1_PR.tpr

I get a warning which reads:

WARNING 1 [file 1DU9_mod1.top, line 1651]:
 With twin-range cut-off's and SHAKE the virial and the pressure are
 incorrect.

However,  when I delete the constraint_algorithm and shake_tol prameters
from the mdp file allowing grompp to use the defualt LINCS algorithm, grompp
doesn't complaint.

Can any one help me as to why grompp complains when SHAKE is used but not
with LINCS? The forcefield paper used SHAKE as constraint algorithm. Should
I stay with SHAKE or use LINCS instead?

By the way I am using GROMOS53A6 force field for the simulation.

Thanks all.

-----
Research Assistant
Sikkim Manipal University DE

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