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<DIV><FONT face=Arial size=2>Dear Mark and gmxers,</FONT></DIV>
<DIV><FONT face=Arial size=2>thanks a lot for your reply.</FONT></DIV>
<DIV><FONT face=Arial size=2>I am checking md.log file after
5-days-computing-time of the same simulations.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>About temperature and pressure I find these
values:</FONT></DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>Temperature Pressure
(bar)</FONT></DIV>
<DIV><FONT face=Arial size=2> 3.54285e+02
6.54609e+01</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Temperature Pressure
(bar)</FONT></DIV></FONT></DIV>
<DIV><FONT face=Arial size=2> 3.52770e+02
-3.39396e+01</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>Temperature Pressure
(bar)</FONT></DIV></FONT></DIV>
<DIV><FONT face=Arial size=2> 3.54570e+02
-4.24080e+01</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Temperature Pressure
(bar)</FONT></DIV>
<DIV><FONT face=Arial size=2> 3.54669e+02
4.29965e+01</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>Temperature Pressure
(bar)</FONT></DIV></FONT></DIV>
<DIV><FONT face=Arial size=2>3.51791e+02 -1.49698e+01</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>And so on...</FONT></DIV>
<DIV><FONT face=Arial size=2>Are these variations ok?</FONT></DIV>
<DIV><FONT face=Arial size=2>I wonder if temperature value ( constantly 2-4K
over the fixed value) can be considered good.</FONT></DIV>
<DIV><FONT face=Arial size=2>And what about pressure variation?</FONT></DIV>
<DIV><FONT face=Arial size=2>I use these options in my NPT
simulations:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial
size=2>Tcoupl
=
Berendsen<BR>tc-grps
= Protein
SOL<BR>tau_t
= 0.1 0.1
;time in
ps<BR>ref_t
= 350 350<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>Pcoupl
=
Berendsen<BR>Pcoupltype =
isotropic<BR>tau_p
= 1.0 <BR>compressibility =
4.5e-5<BR>ref_p
= 1.0</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Should I modify any option in order to obtain a
better convergence?</FONT></DIV>
<DIV><FONT face=Arial size=2>Should I use a different electrostatic treatment
(PME)?</FONT></DIV>
<DIV><FONT face=Arial size=2>Sorry for the long message.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks in advance</FONT></DIV>
<DIV><FONT face=Arial size=2>Marino</FONT></DIV>
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