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<P><FONT size=2>Dear All,<BR><BR>I am doing the simulation of POPE lipid +
Protein, I did my system setup using mdrun_hole program. It looks fine to
me <A
href="http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif">http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif</A> (Figure-A).
When I was doing energy minimization (using steepest decent and conjugant
gradient algorithm), water molecules diffuse a lot, structure looks very weird
(Figure-B). But only after 1ps mdrun (NVT ensemble) it comes back to its normal
(Figure-C). But during this 1ps I got lots of LINCE warning, all for water
molecules. If I continue my simulation (till now ~5ns production run) I do
not get any problem/warning.</FONT></P>
<P><FONT size=2>So I just want to know should I proceed further, or I have to
come back to my initial state and resolve this problem?<BR>Previously I tried
different options by changing value of emtol but I could not resolve this
problem. So I proceeded. By this mail, I am requesting expert comments from you
people. Is it normal to Membrane simulation or there is some problem in my
system? Till now I have not encountered any problems/warning.<BR><BR>Eagerly
waiting for your reply,<BR><BR></FONT></FONT></FONT><FONT size=2><FONT
size=1><FONT size=2>Best regards,<BR>Alok Jain</FONT></FONT></FONT></P><FONT
size=2><FONT size=1><FONT size=2></FONT></FONT></FONT></DIV><FONT size=2><FONT
size=1></FONT></FONT></FONT></DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1></FONT></FONT></FONT> </DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT
size=2>@Mark:</FONT></FONT></FONT></FONT></DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT size=2>Thanks a lot for your
reply/comments and time. I am using TIP4P water model, and I really could not
understand why it happens, Some of the bonds of the water molecules are broken
down, and after 1ps MD they make bonds again. Is it not very strange? I
have tried to visualize in different visualization tool but still problem was
persisting. I was not able to implement your suggestion regarding tolerance
limit of the visualization software, I used rasmol, chimera, insightII but could
not found any such option. I am still trying for that, if I could found it, I
will inform you the result after that. I am really worried about temporary
LINCE warning<BR>which I was getting. Is there any way to resolve this
issue?<BR><BR>I am pasting the em.mdp and my top file
below.</FONT></FONT></FONT></FONT></DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT
size=2></FONT></FONT></FONT></FONT> </DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT size=2>@chris: Thanks for your
time spent on investigating on my problem. Thanks for creating the public album.
I am sorry to say I could not get your statement "In the worst case scenario
that I can imagine, temporary lincs warning could represent a chiral inversion
that will never be resolved and never give you any more warning messages, but
would definitely give you the wrong answer." could you please explain it a
little more (in layman term) because as I think there is no Chiral center in
water so what it<BR>means by chiral inversion.</FONT></FONT></FONT></FONT></DIV>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT size=2>I have also plotted the
two plots to validate my final structure of mdrun_hole program and uploaded
these plots at <A
href="http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg ">http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg </A>
As I pasted below my em.mdp file. I was using FLEXIBLE TIP4P water
molecules.<BR></DIV>
<DIV><BR></DIV></FONT></FONT></FONT></FONT>
<DIV><FONT size=2><FONT size=2><FONT size=1><FONT size=2></FONT> </DIV>
<P><FONT
size=2>em.mdp<BR>----------<BR><BR>define
=
-DFLEXIBLE<BR>constraints
= none<BR>integrator
=
steep<BR>nsteps
= 10000<BR>;<BR>; Energy minimizing
stuff<BR>;<BR>emtol
=
100<BR>emstep
=
0.001<BR>nstcgsteep
= 1000<BR><BR>comm_mode =
Linear<BR>nstcomm
= 1<BR>comm_grps =
Protein_POP
SOL<BR>ns_type =
grid<BR>rlist
= 0.9<BR>coulombtype =
PME<BR>rcoulomb
=
0.9<BR>vdw-type
=
Cut-off<BR>rvdw =
1.2<BR>fourierspacing =
0.12<BR>pme_order =
4<BR>ewald_rtol
= 1e-5<BR>optimize_fft
=
yes<BR>Tcoupl
=
no<BR>Pcoupl
=
no<BR>gen_vel
= no<BR><BR><BR><BR>top file:<BR>--------------<BR><BR>; Include
forcefield parameters<BR>#include "/home/lysine/ffoplsaa.itp"<BR><BR>; Include
chain topologies<BR>#include "Protein_A.itp"<BR>#include
"Protein_B.itp"<BR>#include "Protein_C.itp"<BR>#include
"Protein_D.itp"<BR><BR>#include "pope_opls.itp"<BR><BR>; Include water
topology<BR>#include "tip4p.itp"<BR><BR><BR>#ifdef POSRES_WATER<BR>; Position
restraint for each water oxygen<BR>[ position_restraints ]<BR>; i
funct
fcx
fcy fcz<BR>
1 1
10000 10000
10000<BR>#endif<BR><BR>; Include generic topology for ions<BR>#include
"ions.itp"<BR><BR>[ system ]<BR>; Name<BR>protein + POPE + TIP4P water
molecules<BR><BR>[ molecules ]<BR>;
Compound
#mols<BR>Protein_A
1<BR>Protein_B
1<BR>Protein_C
1<BR>Protein_D
1<BR>POPE
269<BR>SOL
13800</FONT><BR><BR></P>
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