<p>Hi D_Roy,</p>
<p>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.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Mar 17, 2012 10:31 AM, "D_Roy" <<a href="mailto:r.dipankar@gmail.com">r.dipankar@gmail.com</a>> wrote:<br><br>I trying to do an NVT simulation of a peptide in water with the following mdp<br>
parameters:<br>
<br>
====<br>
title = GROMOS53A6 NVT equilibration<br>
define = -DPOSRES ; position restrain the protein<br>
<br>
; Run parameters<br>
integrator = md ; leap-frog integrator<br>
nsteps = 50000 ; 2 * 50000 = 100 ps<br>
dt = 0.002 ; 2 fs<br>
<br>
; Output control<br>
nstxout = 100 ; save coordinates every 0.2 ps<br>
nstvout = 100 ; save velocities every 0.2 ps<br>
nstxtcout = 100 ; save coordinates to trajectory every 0.2 ps<br>
nstenergy = 100 ; save energies every 0.2 ps<br>
nstlog = 100 ; update log file every 0.2 ps<br>
<br>
; Bond parameters<br>
continuation = no ; first dynamics run<br>
<br>
;bond constraint<br>
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>
constraint_algorithm = SHAKE ;<br>
shake_tol = 0.0001 ; relative tolerance<br>
<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cells<br>
nstlist = 5 ; 10 fs<br>
rlist = 0.8 ; short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)<br>
<br>
; Electrostatics and ven der Waals<br>
coulombtype = Reaction-Field ; reaction-field for long-range<br>
electrostatics<br>
vdw-type = Cut-off ; van der Waals treatment for long-range<br>
electrostatics<br>
epsilon_rf = 62 ; dielectric constant/relative permitivitty<br>
<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc-grps = Protein Non-Protein ; two coupling groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 ; reference temperature, one for each group, in<br>
K<br>
<br>
; Pressure coupling is off<br>
pcoupl = no ; no pressure coupling in NVT<br>
<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
<br>
; Dispersion correction<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
<br>
; Velocity generation<br>
gen_vel = yes ; assign velocities from Maxwell distribution<br>
gen_temp = 300 ; temperature for Maxwell distribution<br>
gen_seed = -1 ; generate a random seed<br>
<br>
==========<br>
When I run grompp with the command:<br>
<br>
grompp -v -f pr.mdp -c protein_mod1_EM_solv.gro -p protein_mod1.top -o<br>
protein_mod1_PR.tpr<br>
<br>
I get a warning which reads:<br>
<br>
WARNING 1 [file 1DU9_mod1.top, line 1651]:<br>
With twin-range cut-off's and SHAKE the virial and the pressure are<br>
incorrect.<br>
<br>
However, when I delete the constraint_algorithm and shake_tol prameters<br>
from the mdp file allowing grompp to use the defualt LINCS algorithm, grompp<br>
doesn't complaint.<br>
<br>
Can any one help me as to why grompp complains when SHAKE is used but not<br>
with LINCS? The forcefield paper used SHAKE as constraint algorithm. Should<br>
I stay with SHAKE or use LINCS instead?<br>
<br>
By the way I am using GROMOS53A6 force field for the simulation.<br>
<br>
Thanks all.<br>
<br>
-----<br>
Research Assistant<br>
Sikkim Manipal University DE<br>
<br>
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