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<DIV><FONT face=Arial size=2>Hi all,</FONT></DIV>
<DIV><FONT face=Arial size=2>sorry for the long mail.</FONT></DIV>
<DIV><FONT face=Arial size=2>I am performing two
different 45ps NPT equilibrations of an oligopeptide in water solvent
(33157 system atoms),</FONT><FONT face=Arial size=2> one with a temperature of
350K and the second one at 400K.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am using this mdp with the gromos96 ff
:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>cpp = /lib/cpp</FONT></DIV>
<DIV><FONT face=Arial size=2>define = -DFLEX_SPC ; NPT 50 ps all
free</FONT></DIV>
<DIV><FONT face=Arial size=2>constraints = all-bonds</FONT></DIV>
<DIV><FONT face=Arial size=2>constraint_algorithm= lincs</FONT></DIV>
<DIV><FONT face=Arial size=2>lincs_order = 8</FONT></DIV>
<DIV><FONT face=Arial size=2>integrator = md</FONT></DIV>
<DIV><FONT face=Arial size=2>dt = 0.0015</FONT></DIV>
<DIV><FONT face=Arial size=2>nsteps = 30000 ; total 45 ps.</FONT></DIV>
<DIV><FONT face=Arial size=2>nstxout = 6000</FONT></DIV>
<DIV><FONT face=Arial size=2>nstvout = 6000</FONT></DIV>
<DIV><FONT face=Arial size=2>nstfout = 0</FONT></DIV>
<DIV><FONT face=Arial size=2>nstlog = 6000</FONT></DIV>
<DIV><FONT face=Arial size=2>nstenergy = 500</FONT></DIV>
<DIV><FONT face=Arial size=2>nstxtcout = 6000</FONT></DIV>
<DIV><FONT face=Arial size=2>nstlist = 5</FONT></DIV>
<DIV><FONT face=Arial size=2>ns_type = grid</FONT></DIV>
<DIV><FONT face=Arial size=2>rlist = 0.8</FONT></DIV>
<DIV><FONT face=Arial size=2>coulombtype = cut-off</FONT></DIV>
<DIV><FONT face=Arial size=2>rcoulomb = 1.4</FONT></DIV>
<DIV><FONT face=Arial size=2>rvdw = 1.4</FONT></DIV>
<DIV><FONT face=Arial size=2>pbc = xyz</FONT></DIV>
<DIV><FONT face=Arial size=2>DispCorr = EnerPres</FONT></DIV>
<DIV><FONT face=Arial size=2>; Berendsen temperature coupling is on in two
groups</FONT></DIV>
<DIV><FONT face=Arial size=2>Tcoupl = Berendsen</FONT></DIV>
<DIV><FONT face=Arial size=2>tc-grps = Protein SOL</FONT></DIV>
<DIV><FONT face=Arial size=2>tau_t =
0.1 0.1 ;time in
ps</FONT></DIV>
<DIV><FONT face=Arial size=2>ref_t =
400 400</FONT></DIV>
<DIV><FONT face=Arial size=2>; Energy monitoring</FONT></DIV>
<DIV><FONT face=Arial size=2>energygrps = Protein SOL</FONT></DIV>
<DIV><FONT face=Arial size=2>; Isotropic pressure coupling is now
on</FONT></DIV>
<DIV><FONT face=Arial size=2>Pcoupl = Berendsen</FONT></DIV>
<DIV><FONT face=Arial size=2>Pcoupltype = isotropic</FONT></DIV>
<DIV><FONT face=Arial size=2>tau_p = 1.0 ;time in ps</FONT></DIV>
<DIV><FONT face=Arial size=2>compressibility = 4.5e-5</FONT></DIV>
<DIV><FONT face=Arial size=2>ref_p = 1.0</FONT></DIV>
<DIV><FONT face=Arial size=2>; Generate velocites is off at 400
K.</FONT></DIV>
<DIV><FONT face=Arial size=2>gen_vel = yes</FONT></DIV>
<DIV><FONT face=Arial size=2>gen_temp = 400.0</FONT></DIV>
<DIV><FONT face=Arial size=2>gen_seed = 173529</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>And the same one mdp file with 350K (ref_t
and gen_temp).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Checking the md.log file I find in AVERAGES
section:</FONT></DIV>
<DIV><FONT face=Arial size=2>- for 400K md: </FONT><FONT
size=2>Temperature <FONT size=2>4.03243e+02</FONT> <FONT face=Arial>
and </FONT> </FONT><FONT size=2><FONT size=2>Pressure (bar) <FONT
size=2>2.50459e+00 </FONT></FONT></FONT></DIV>
<DIV><FONT size=2><FONT size=2><FONT face=Arial>- for 350K md: </FONT><FONT
face="Times New Roman">Temperature <FONT size=2>3.53436e+02<FONT
face=Arial> and</FONT><FONT face="Times New Roman"> Pressure
(bar) <FONT size=2>1.51139e+00</FONT></FONT></FONT></FONT></DIV></FONT></FONT>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Can anyone tell me if this average values are ok
for these kind of simulations?</FONT></DIV>
<DIV><FONT face=Arial size=2>If not, how can I obtain more precision in these
analysis?</FONT></DIV>
<DIV><FONT face=Arial size=2>Thank a lot.</FONT></DIV>
<DIV><FONT face=Arial size=2>Marino Convertino</FONT> </DIV></BODY></HTML>