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<DIV>Dear all,</DIV>
<DIV> </DIV>
<DIV>As you suggested, to use Gromacs 3.2.1 for continuing trajectory. It seems to be good that all the energies and some properties are equal, except pressure. You can see below that i mark the pressure value. Is it significant ? and how can i do to adjust the pressure which will be equal as the other properties. (And the next is my input file that i use) </DIV>
<DIV> </DIV>
<DIV><STRONG><U>the previous file</U></STRONG></DIV>
<DIV> Step Time Lambda<BR> 500000 1000.00006 0.00000</DIV>
<DIV> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.080067 14445 14446 0.025450<BR> After LINCS 0.000122 404 407 0.000008</DIV>
<DIV> Energies (kJ/mol)<BR> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<BR> 2.00835e+04 2.56519e+03 4.14071e+03 8.06361e+02 3.94693e+03<BR> Coulomb-14 LJ (SR) Coulomb (SR) Coulomb (LR) Potential<BR> 1.95655e+04 1.31344e+03 -2.14504e+05 -1.01600e+05 -2.63682e+05<BR> Kinetic En. Total Energy Temperature <STRONG><EM><U>Pressure (bar)<BR></U></EM></STRONG> 4.58780e+04 -2.17805e+05 3.12032e+02
<EM><U><STRONG>1.52697e+02<BR></STRONG></U></EM> </DIV>
<DIV><U><STRONG>the 2nd file</STRONG></U></DIV>
<DIV>Energies (kJ/mol)<BR> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<BR> 2.00835e+04 2.56519e+03 4.14071e+03 8.06361e+02 3.94693e+03<BR> Coulomb-14 LJ (SR) Coulomb (SR) Coulomb (LR) Potential<BR> 1.95655e+04 1.31344e+03 -2.14504e+05 -1.01600e+05 -2.63682e+05<BR> Kinetic En. Total Energy Temperature <EM><STRONG><U>Pressure (bar)<BR></U></STRONG></EM> 4.58780e+04 -2.17805e+05 3.12032e+02 <STRONG><EM><U>1.52337e+02</U></EM></STRONG></DIV>
<DIV> Step Time Lambda<BR> 500100 1000.20007 0.00000</DIV>
<DIV>....................................................................................................................................</DIV>
<DIV><STRONG><U>My input file:</U></STRONG></DIV>
<DIV>title = M2 in dmPC<BR>cpp = /lib/cpp<BR>constraints = all-bonds<BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 500000 ; total 1000 ps = 1 ns !<BR>nstcomm = 1<BR>nstxout = 250<BR>nstvout =
1000<BR>nstfout = 0<BR>nstlog = 100<BR>nstenergy = 100<BR>nstlist = 10<BR>ns_type = grid<BR>rlist = 1.2<BR>coulombtype = PME<BR>rcoulomb = 1.2<BR>rvdw = 1.2<BR>pbc = xyz<BR>; Berendsen temperature
coupling is on in two groups<BR>Tcoupl = berendsen<BR>tc-grps = Protein DMPC SOL Na<BR>tau_t = 0.1 0.1 0.1 0.1<BR>ref_t = 310 310 310 310<BR>; Energy monitoring<BR>energygrps = Protein DMPC SOL Na<BR>; Isotropic pressure coupling is now on<BR>Pcoupl = berendsen<BR>Pcoupltype =
isotropic<BR>tau_p = 1.0<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>; Generate velocites is off at 300 K.<BR>gen_vel = no<BR>gen_temp = 310.0<BR></DIV></DIV><p>
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