Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? And why does this curvature of the membrane occurs?<div><br></div><div>Thanks a lot once again.</div><div><br></div><div>
Regards,</div><div><br></div><div>Anirban<br><br><div class="gmail_quote">On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Although a bit worrying the curvature of your bilayer is not<br>
responsible for the error message you are seeing.<br>
<br>
to solve the problem you have to increase to use the -rrd option<br>
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should<br>
be fine.<div><div></div><div class="h5"><br>
<br>
On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
Hi ALL,<br>
<br>
I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error:<br>
<br>
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
Energies (kJ/mol)<br>
Bond G96Angle Proper Dih. Improper Dih. LJ (SR)<br>
4.73694e+04 3.00928e+04 4.68451e+03 8.26028e+02 -1.29727e+06<br>
Coulomb (SR) Potential Kinetic En. Total Energy Temperature<br>
-7.97216e+03 -1.22227e+06 2.24656e+05 -9.97613e+05 3.21675e+02<br>
Pressure (bar) Cons. rmsd ()<br>
-9.97540e+00 1.69233e-05<br>
<br>
<br>
Not all bonded interactions have been properly assigned to the domain decomposition cells<br>
<br>
A list of missing interactions:<br>
G96Angle of 28064 missing 1<br>
<br>
Molecule type 'DSPC'<br>
the first 10 missing interactions, except for exclusions:<br>
G96Angle atoms 10 11 12 global 5309 5310 5311<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.0.7<br>
Source code file: domdec_top.c, line: 341<br>
<br>
Fatal error:<br>
1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br>
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as:<br>
<br>
--------------------------------------------------------------------------------------------------------------<br>
[ system ]<br>
PROT in DSPC Bilayer<br>
<br>
[ molecules ]<br>
Protein 1<br>
DSPC 104<br>
W 1397<br>
NA+ 0<br>
CL- 4<br>
Protein 1<br>
DSPC 104<br>
W 1397<br>
NA+ 0<br>
CL- 4<br>
-------------------------------------------------------------------------------------------------------------<br>
<br>
How can I resolve this error? Any suggestion is welcome.<br>
<br>
Regards,<br>
<br>
Anirban<br></div></div>
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