Hi:<br><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Thanks to everybody who helped me out with my last email. But now I
have another problem and I hope you can help me. As i told you I'm
doing a simulation of polyelectrolyte chain consisting of 50 charged
beads (-1) with 50 charged counterions(+1). My box
simulation is 400 nm x 400 nm x 400 nm and the polyelectrolyte
length is 100 nm. My problem is when I chage the intregator md to bd
(position langevin dynamics), it gives me <font style="font-weight: bold;" size="2"> Large VCM (group System)</font><meta name="Generator" content="Kate, the KDE Advanced Text Editor"> in the md.log file and after some time
<font class="contentText">it
crashes at some point. When i take a look at the energy file and plot
the temperature I realized that the temperature is far from the desired
temperature. Please take a look at my mdp file and help me figure out
what i'm doing wrong. <br>
My last question how can I choose the rlist, Vdw and coulomb
cut-off when I'm using PME and , for example my case in </font><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta name="Generator" content="Kate, the KDE Advanced Text Editor"> 400 nm x 400 nm x 400 nm and 100 atoms with
fourierspacing = 20 (is it ok?). Thanks in advance.<br>
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<meta name="Generator" content="Kate, the KDE Advanced Text Editor">
<pre><font size="4">; By user: pcl<br>; VARIOUS PREPROCESSING OPTIONS<br>title = Yo<br>cpp = /lib/cpp<br>include = <br>define = <br><br>; RUN CONTROL PARAMETERS
<br>integrator = bd<br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.0001<br>nsteps = 100000000<br> <br>comm-mode = Linear
<br>nstcomm = 1<br>comm-grps = System<br><br>; LANGEVIN DYNAMICS OPTIONS<br>; Friction coefficient (amu/ps) and random seed<br>bd-fric = 0.05 <br>ld_seed = 1993
<br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>nstlist = 10 ;<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)or full (infinite systems only)
<br>pbc = xyz<br>; nblist cut-off <br>rlist = 100<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>;rcoulomb-switch = 0
<br>rcoulomb = 100<br>fourierspacing = 20<br>optimize_fft = yes<br>; Relative dielectric constant for the medium and the reaction field<br>epsilon_r = 13.89354; <br>; Method for doing Van der Waals
<br>vdw-type = Cut-off <br>rvdw-switch = 0<br>rvdw = 100<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling <br>Tcoupl = Berendsen
<br>; Groups to couple separately<br>tc-grps = NA POL<br>; Time constant (ps) and reference temperature (K)<br>tau_t = 0.01 0.01<br>ref_t = 120.2717 120.2717; <br><br>
; Pressure coupling <br>Pcoupl = no<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = no<br><br>; OPTIONS FOR BONDS <br>constraints = none</font>
</pre><br>-- <br>Cheers, <br> <br>Paul <br>National Tsing Hua University (ÇåÈA´óŒW)<br><br>ÖxÖxÄãµÄŽÍæ<br>I appreciate your help. Thanks!<br>Os agradezco la ayuda. Gracias!
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