<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear users:</DIV>
<DIV> I am simulating a CNT in water. In the energy minimization step, I <SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US> restrain the CNT by a constant 10e8,because I don't want the CNT to deform.</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>After minimization,the energy is -44054.835938. Then NVT and NPT equilibration , at this step,the end C atoms are fixed by a constant 300000 to prevent from being swept away. The temperature is OK. But the pressure may be not so proper.It is larger than the set value.It is OK?</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US><FONT size=2>Energy Average RMSD Fluct. Drift Tot-Drift<BR>-------------------------------------------------------------------------------<BR>Pressure (bar) 1.5674 6891.48 6891.42 -0.100337 -100.337</FONT></SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US><FONT size=2>the npt.mdp</FONT></SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>title = OPLS Lysozyme NPT equilibration <BR>define = -DPOSRES ; position restrain the protein<BR>; Run parameters<BR>integrator = md ; leap-frog integrator<BR>nsteps = 500000 ; 2 * 50000 = 100 ps<BR>dt = 0.002 ; 2 fs<BR>; Output control<BR>nstxout = 100 ; save coordinates every 0.2 ps<BR>nstvout = 100 ; save velocities every 0.2 ps<BR>nstenergy = 100 ; save energies every 0.2 ps<BR>nstlog = 100 ; update log file every 0.2 ps<BR>; Bond parameters<BR>continuation = yes ; Restarting after NVT <BR>constraint_algorithm = lincs ; holonomic constraints
<BR>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<BR>lincs_iter = 1 ; accuracy of LINCS<BR>lincs_order = 4 ; also related to accuracy<BR>; Neighborsearching<BR>ns_type = grid ; search neighboring grid cels<BR>nstlist = 5 ; 10 fs<BR>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<BR>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<BR>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<BR>; Electrostatics<BR>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<BR>pme_order = 4 ; cubic interpolation<BR>fourierspacing = 0.16 ; grid spacing for FFT<BR>; Temperature coupling is on<BR>tcoupl = V-rescale ; modified Berendsen thermostat<BR>tc-grps = CNT SOL ; two coupling groups
- more accurate<BR>tau_t = 0.1 0.1 ; time constant, in ps<BR>ref_t = 300 300 ; reference temperature, one for each group, in K<BR>; Pressure coupling is on<BR>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<BR>pcoupltype = isotropic ; uniform scaling of box vectors<BR>tau_p = 2.0 ; time constant, in ps<BR>ref_p = 1.0 ; reference pressure, in bar<BR>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<BR>; Periodic boundary conditions<BR>pbc = xyz ; 3-D PBC<BR>; Dispersion correction<BR>DispCorr = EnerPres ; account for cut-off vdW scheme<BR>; Velocity generation<BR>gen_vel = no ; Velocity generation is off <BR></SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US> pressure </SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US> 0.000000 -777.187622<BR> 0.200000 4527.866211<BR> 0.400000 -7984.377930<BR> 0.600000 5585.704102<BR> 0.800000 2807.166992<BR> 1.000000 -3545.817383<BR> 1.200000 4112.207031<BR> 1.400000 2340.378906<BR> 1.600000 -5803.378906<BR> 1.800000 8399.341797<BR> 2.000000 622.575745<BR> 2.200000 -3483.511963<BR> 2.400000 5920.053711<BR> 2.600000 -1108.013306<BR> 2.800000 -4201.218750<BR> 3.000000
5663.891602<BR> 3.200000 -4298.212402<BR> 3.400000 -1245.458862<BR>.....</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>996.400024 -2921.789062<BR> 996.600037 3155.833008<BR> 996.800049 2046.963623<BR> 997.000061 -3057.696045<BR> 997.200073 2390.562500<BR> 997.400024 3122.586182<BR> 997.600037 -254.417053<BR> 997.800049 -741.921631<BR> 998.000061 -1757.483154<BR> 998.200073 -1241.035278<BR> 998.400024 15.855911<BR> 998.600037 316.152985<BR> 998.800049 1165.281250<BR> 999.000061 1776.868286<BR> 999.200073 55.826385<BR> 999.400024 538.847107<BR> 999.600037 4052.162842<BR> 999.800049 -6294.055664<BR> 1000.000061
-1811.536377<BR>Thanks!</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 13.5pt; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>Zhongjin He</DIV>
<DIV><BR></DIV></SPAN></td></tr></table><br>