<DIV>Dear Moeed,</DIV>
<DIV> You seem to be encountering same problem to mine, which was posted to this list, .titled "Unexpected results arising from T- and P-coupling methods". Some gmxers responded it. You can look for and see them. I wish they can be helpful to deal with your problem.</DIV>
<DIV> </DIV>
<DIV>Chaofu Wu, Dr.</DIV>
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<DIV style="FONT-FAMILY: Verdana; COLOR: #000; FONT-SIZE: 14px"></DIV></SIGN>Date: Wed, 13 Apr 2011 20:22:02 -0400<BR>From: Moeed <<A href="mailto:lecielll@googlemail.com" target=_blank><FONT color=#1e5494>lecielll@goo<WBR>glemail.com</FONT></A>><BR>Subject: [gmx-users] NPT issue in 4.0.7 and 4.5.3<BR>To: <A href="mailto:gmx-users@gromacs.org" target=_blank><FONT color=#1e5494>gmx-users@gr<WBR>omacs.org</FONT></A><BR>Message-ID: <<A href="mailto:BANLkTimHFgwpUy6V5OGkAi_JBS2OzfwsQA@mail.gmail.com" target=_blank><FONT color=#1e5494>BANLkTimHFgw<WBR>pUy6V5OGkAi_<WBR>JBS2OzfwsQA@<WBR>mail.gmail.c<WBR>om</FONT></A>><BR>Content-Type: text/plain; charset="iso-8859-1"<BR><BR>Hello,<BR><BR>I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2<BR>SI and box size is 15 nm), one with version 4.0.7 and the other trial using<BR>4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is<BR>giving density of above 600SI (4.0.7) and the other density of around 15 SI<BR>(4.5.3). With 4.5.3 applying 100 bar pressure does not comrades the system<BR>either to the desired density. I need to study the system at different<BR>pressures from 1 to 70 bar, and I am wondering if the system can not be<BR>compressed with these ref_p values how can I keep the pressure fixed at P <<BR>70 bar!?<BR><BR>Please help if you have any idea on why these two versions are giving<BR>inconsistent results and which one is reliable.<BR><BR>Thanks so much,<BR><BR><BR>4.0.7<BR><BR>Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps ],* 14 data sets<BR>The term 'Cons. rmsd ()' is averaged over 2501 frames<BR>All other averages are exact over 250001 steps<BR><BR>Energy Average RMSD Fluct. Drift<BR>Tot-Drift<BR>-------------------------------------------------------------------------------<BR>Angle 36.9945 0.806738 0.804483 0.0521993<BR>0.208798<BR>Ryckaert-Bell. 9.04227 0.376253 0.371412 0.0521057<BR>0.208424<BR>LJ-14 5.23048 0.119612 0.119611 0.00033983<BR>0.00135933<BR>Coulomb-14 -1.66329 0.104171 0.102175 0.0175753<BR>0.0703015<BR>LJ (SR) -27.3967 0 0 0.0421934<BR>0.168774<BR>Coulomb (SR) 8.98711 0.163579 0.16062 -0.0268199<BR>-0.10728<BR>Potential 31.1944 0 0 0.137594<BR>0.550377<BR>Kinetic En. 51.1009 0.987759 0.987724 0.00725949<BR>0.0290381<BR>Total Energy 82.2953 0 0 0.144851<BR>0.579408<BR>Temperature 299.98 5.79849 5.79828 0.000340897<BR>0.170449<BR>*Pressure (bar) 69.3587 414.279 414.256 0.0298385<BR>14.9193*<BR>Cons. rmsd () 4.01744e-06 1.41883e-07 1.41883e-07<BR>0 0<BR>*Box-X 3.04882 0 0 3.57512e-06<BR>0.00178757<BR>Box-Y 3.04882 0 0 3.57512e-*<BR><BR><BR>-----------------------------<BR>4.5.3.<BR><BR>[* 1500.0001 thru 2000.0001 ps ],*<BR><BR>Energy Average Err.Est. RMSD Tot-Drift<BR>-------------------------------------------------------------------------------<BR>Angle 37.1357 0.071 0.812307 -0.099711<BR>(kJ/mol)<BR>Ryckaert-Bell. 9.17677 0.14 0.445934 -0.529281<BR>(kJ/mol)<BR>LJ-14 5.18878 0.0087 0.137673 -0.03119<BR>(kJ/mol)<BR>Coulomb-14 -1.60372 0.051 0.126405 -0.144403<BR>(kJ/mol)<BR>LJ (SR) -4.24478 0.29 0.742141 0.697187<BR>(kJ/mol)<BR>Coulomb (SR) 8.97451 0.082 0.198278 0.232025<BR>(kJ/mol)<BR>Potential 54.6272 0.31 1.20733 0.124627<BR>(kJ/mol)<BR>Kinetic En. 51.1047 0.021 0.9945 -0.066306<BR>(kJ/mol)<BR>Total Energy 105.732 0.31 1.58869 0.058321<BR>(kJ/mol)<BR>Temperature 300.002 0.12 5.83806 -0.389239 (K)<BR>*Pressure 66.734 5.3 91.83 11.5294 (bar)<BR>*<BR>Constr. rmsd 2.2661e-10 2.3e-10 3.58302e-08 -1.3595e-09 ()<BR>*Box-X 11.0055 0.082 0.175309 -0.496198 (nm)<BR>Box-Y 11.0055 0.082 0.175309 -0.496198 (nm)*<BR><BR><BR><BR><BR><BR><BR>pbc = xyz<BR><BR>integrator = md<BR>dt = 0.002<BR>nsteps = 1000000<BR>nstcomm = 100<BR>nstenergy = 100<BR>nstxout = 100<BR><BR>nstlist = 10<BR>ns_type = grid<BR><BR>coulombtype = Shift<BR>vdw-type = Shift<BR>rcoulomb-switch = 0<BR>rvdw-switch = 0.9<BR>rlist = 1.2<BR>rcoulomb = 1.2<BR>rvdw = 1.0<BR><BR>Tcoupl = v-rescale<BR>tc-grps = System<BR>tau_t = 0.1<BR>ref_t = 300<BR><BR><BR>Pcoupl = berendsen<BR>Pcoupltype = isotropic<BR>tau_p = 1<BR>compressibility = 4.5e-5 4.5e-5<BR>ref_p = 70<BR><BR><BR>gen_vel = yes<BR>gen_temp = 300.0<BR>gen_seed = 173529<BR><BR><BR>constraints = all-bonds<BR>constraint-algorithm = lincs<BR><BR></DIV>