<BLOCKQUOTE style="BORDER-BOTTOM: medium none; BORDER-LEFT: black 1.5pt solid; PADDING-BOTTOM: 0mm; MARGIN: 5pt 0mm 5pt 3.75pt; PADDING-LEFT: 4pt; PADDING-RIGHT: 0mm; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0mm"><BR>
<DIV style="FONT: 9pt 宋体"><FONT color=#717475 face=Verdana><A title="" href="mailto:csy12@mails.jlu.edu.cn" target=_blank>csy12@mails.jlu.edu.cn</A></FONT></DIV>
<P style="FONT: 9pt 宋体"> </P>
<BLOCKQUOTE style="BORDER-BOTTOM: medium none; BORDER-LEFT: black 1.5pt solid; PADDING-BOTTOM: 0mm; MARGIN: 5pt 0mm 5pt 3.75pt; PADDING-LEFT: 4pt; PADDING-RIGHT: 0mm; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0mm">
<P> </P>
<P>Dear gromacs users:</P>
<P></P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">I have an issue when I calculate the viscosity with NEMD.</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">Why the value of 1/viscosity obtained by g_energy in GROMACS remains zero when calculating viscosity with NEMD?</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">The mdp file is below:</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">title = production-run<BR>cpp = /lib/cpp<BR>define =<BR>constraints =<BR>integrator = md<BR>dt = 0.001 ; ps !<BR>nsteps = 80000<BR>nstcomm = 1<BR>nstxout = 100<BR>nstvout = 100<BR>nstxtcout = 5000<BR>nstfout = 0<BR>nstlog = 10000<BR>nstenergy = 100<BR>nstlist = 1<BR>ns_type = grid<BR>; Periodic boundary conditions: xyz or no =<BR>pbc = xyz<BR>rlist = 1.3<BR>rcoulomb = 1.3<BR>rvdw = 1.3</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px" id=yui_3_14_1_1_1423573895619_1903>; OPTIONS FOR ELECTROSTATICS AND VDW =<BR>; Method for doing electrostatics =<BR>coulombtype = PME<BR>; Method for doing Van der Waals =<BR>;;;;;;;;;;;;;vdw-type = Switch<BR>; cut-off lengths =<BR>;;;;;;;;;;;;;;;;rvdw-switch = 1.3<BR>; Apply long range dispersion corrections for Energy and Pressure =<BR>DispCorr = EnerPres<BR>; Spacing for the PME/PPPM FFT grid =<BR>fourierspacing = 0.08<BR>; FFT grid size, when a value is 0 fourierspacing will be used =<BR>fourier_nx = 0<BR>fourier_ny = 0<BR>fourier_nz = 0<BR>; EWALD/PME/PPPM parameters =<BR>pme_order = 6<BR>ewald_rtol = 1e-05<BR>ewald_geometry = 3d<BR>epsilon_surface = 0<BR>optimize_fft = yes<BR>; Nose-Hoover temperature coupling is on<BR>Tcoupl = berendsen<BR>tc-grps = PF6 c10<BR>tau_t = 0.05 0.05<BR>ref_t = 300.00 300.00<BR>; Energy monitoring<BR>energygrps = PF6 c10<BR>; Pressure coupling is on<BR>Pcoupl = no<BR>tau_p = 1.0<BR>;Non-equlibrium MD<BR>cos_acceleration = 0.06<BR>; Generate velocites is on at 300 K.</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">gen_vel = no</P>
<P style="TEXT-ALIGN: left; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(247,247,244); TEXT-INDENT: 0px; MARGIN: 0px 0px 10px; PADDING-RIGHT: 0px; FONT: 14px/21px 'Helvetica Neue', Helvetica, Arial, sans-serif; WHITE-SPACE: normal; LETTER-SPACING: normal; COLOR: rgb(68,68,68); WORD-SPACING: 0px; -webkit-text-stroke-width: 0px">gen_temp = 300.00<BR>gen_seed = 273529</P></BLOCKQUOTE></BLOCKQUOTE><!-- end sanitized html -->