I've found main reason of such crushes. It was due to the individual internal waters wich I've included to my model as the buried to the protein interiour ( the coordinates were copppied form X-ray structure of the same protein). <br>
<br>By the way I have already performed the same simulation with the inclussion of the same X-ray waters but in different system with membrane-mimicking env. consisted of Ccl4 in water. As the result there have not been any problems with that system.<br>
<br>Finally I have some question about G_membed acceleration. I've noticed that the process of insertion of the protein in the membrane is very long (actually it's only 50ps simulation).<br><br>During procesing of my system I've obtained notes like<br>
<br>NOTE 4 [file topol.top, line 19511]:<br> For energy conservation with LINCS, lincs_iter should be 2 or larger.<br><br>NOTE 1 [file gmembed.mdp]:<br> You are using a cut-off for VdW interactions with NVE, for good energy<br>
conservation use vdwtype = Shift (possibly with DispCorr)<br><br>NOTE 2 [file gmembed.mdp]:<br> You are using a cut-off for electrostatics with NVE, for good energy<br> conservation use coulombtype = PME-Switch or Reaction-Field-zero<br>
<br>The parameters for long-range and short-range interactions I've used from my typical simulation on the lipid Gromos56-ff ( presented in the Justin's tutorial).<br><br>Is there any other parameters for that object wich are most suitable for G_membed ?<br>
<br>James<br><br><br><div class="gmail_quote">2012/6/14 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark,<br><br>I've used commands provided in the G_membed manual<br><br> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 <br><br>or<br><br> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100<br>
<br><br>In both cases I've obtained the same message<br><br>There are 122 lipids in the membrane part that overlaps the protein.<br>The area per lipid is 0.5002 nm^2.<br>Maximum number of lipids that will be removed is 45.<br>
<br>and eventually only 10 lipids were removed. Also I've tried to do this on another pope bilayer (consisted of bigger lipids with properly equilirated ) but I've obtained exactly the same results.<br><br><br>James<br>
<br><div class="gmail_quote">2012/6/14 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div class="h5">
<div bgcolor="#FFFFFF" text="#000000"><div>
On 14/06/2012 4:39 PM, James Starlight wrote:
<blockquote 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></div>
You've asked about this before... <a href="http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html</a><div>
<br>
<br>
<blockquote 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></div>
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.<span><font color="#888888"><br>
<br>
Mark</font></span><div><div><br>
<br>
<blockquote 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>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
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