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On 14/06/2012 4:39 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzUHcNrjnAfKEAO-PaP=XbuBQ+LKxYLg0f+nWJCpEsM7w@mail.gmail.com"
type="cite">Dear Gromacs Users!<br>
<br>
I've forced with the problem durin insertion of my protein into
pre-equilibrated bilayer via G_Membed. <br>
<br>
I've done all steps in accordance to the KALP tutorial ( I've
oriented both membrane as well as the protein in the same
dimensions merged both topologies and gro files in the merged.gro
file ) but after processed via grompp I've recieved warning<br>
<br>
WARNING 1 [file gmembed.mdp]:<br>
Can not exclude the lattice Coulomb energy between energy groups<br>
</blockquote>
<br>
You've asked about this before... <a
href="http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html">http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html</a><br>
<br>
<blockquote
cite="mid:CAALQopzUHcNrjnAfKEAO-PaP=XbuBQ+LKxYLg0f+nWJCpEsM7w@mail.gmail.com"
type="cite">if I scip this message by maxwarn oprtins, g_membed
remove only 10 lipids ( while > 40 are overlapped with the
protein ) and during further g_membed's md_run I've obtained lincs
warning and my system is crushed .<br>
</blockquote>
<br>
Have you followed g_membed -h and their published method? You've not
shown your command lines, so it's impossible for anyone to know what
you're doing.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzUHcNrjnAfKEAO-PaP=XbuBQ+LKxYLg0f+nWJCpEsM7w@mail.gmail.com"
type="cite">
<br>
<br>
I'm using berger lipids and that mdp file for the G_membed<br>
<br>
integrator = md<br>
energygrps = Protein<br>
freezegrps = Protein<br>
freezedim = Y Y Y<br>
energygrp_table<br>
energygrp_excl = Protein Protein<br>
<br>
<br>
<br>
emtol = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>
nsteps = 50000 ; Maximum number of (minimization)
steps to perform<br>
<br>
; Bond parameters<br>
constraint_algorithm = lincs ; holonomic constraints <br>
constraints = all-bonds ; all bonds (even heavy
atom-H bonds) constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cels<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.2 ; short-range neighborlist cutoff (in
nm)<br>
rcoulomb = 1.2 ; short-range electrostatic cutoff (in
nm)<br>
rvdw = 1.2 ; short-range van der Waals cutoff (in
nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
pbc = xyz ; 3-D PBC<br>
<br>
<br>
Could you tell me where is the problem in my case might be?<br>
<br>
<br>
James<br>
<br>
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<br>
</blockquote>
<br>
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