The system is a protein binding with one ligand and the ligand mutates
to another one. The problem is found when lamda=1. First of all I run a
energy minimization using an initial structure from the product of
lamda=0.9. Then the problem happens when I run a equilibrium. <br>
Here is the mdp option:<br>
cpp
=/usr/bin/cpp<br>
integrator
=
md
<br>
tinit = 0<br>
dt
= 0.002<br>
nsteps = 50000<br>
nstcomm = 1<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 500<br>
nstenergy
=
100
<br>
nstxtcout = 5000<br>
xtc-precision = 1000<br>
nstlist = 1<br>
ns_type = grid<br>
<br>
Pcoupl = berendsen<br>
tau_p = 1.0<br>
compressibility = 4.5e-05<br>
ref_p = 1.0<br>
<br>
tcoupl = nose-hoover<br>
tc_grps = system<br>
tau_t = 0.1<br>
ref_t = 300<br>
<br>
constraints = none<br>
constraint-algorithm =
lincs
<br>
shake-tol = 0.0001<br>
lincs-order = 12<br>
lincs-warnangle =
30
<br>
coulombtype
=
pme
<br>
rcoulomb
=
1.0
<br>
epsilon-r
=
1
<br>
vdw-type
=
switch
<br>
rvdw-switch = 1.0<br>
rvdw
= 1.3<br>
DispCorr
=
EnerPres
<br>
fourierspacing
=
0.08
<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
<br>
pme_order = 6<br>
ewald_rtol = 1e-05<br>
epsilon_surface = 0<br>
optimize_fft = yes<br>
<br>
free_energy = yes<br>
init_lambda = 1.0<br>
delta_lambda = 0<br>
sc_alpha =0.5<br>
sc-power =1.0<br>
sc-sigma = 0.3<br>
<br><br>
Thanks.<br>
<br>
<br><div><span class="gmail_quote">On 8/8/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Wang Qin wrote:<br>> Dear all,<br>> I am trying to do a FEP. In the equilibrium step, it fails<br>> after about 500 steps with a warnning: pressure scaling more than 1%,<br>> mu: 1.06718 1.06718 1.06718
. I searched the old discussion about it and<br>> then try to increase the tau_p to 2 till 10. But it just goes futher but<br>> still meets the problem at the end.<br>> Any idea about it?<br><br>Not unless you tell us how you prepared this system. Almost certainly
<br>the initial structure is too far from the constant-P equilibrium state.<br>Follow the kind of things that the tutorial material does, and also<br>check out this link<br><a href="http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation">
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation</a><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
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