<HTML>
<HEAD>
<META content="text/html; charset=big5" http-equiv=Content-Type>
<META content="OPENWEBMAIL" name=GENERATOR>
</HEAD>
<BODY bgColor=#ffffff>
<pre>>If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs
>are unheard of and 2-nm grid spacing is about 20 times too large.
>
>Without seeing the original .mdp file that gave the high PME load, and without a
>further description about how large the system is (number of atoms), it is hard
>to say what you should do. Some system do not parallelize well, but I imagine
>you should be able to get better performance.
>
>-Justin
<br />
<br />Thank you for reply
<br />The original .mdp is below and the number of atoms is 20171
<br />The difference is only in rlist, rcoulomb, rvdw, and fourierspacing
<br />
<br /><i>title = ttt
</i><i>cpp = /lib/cpp
</i><i>constraints = hbonds
</i><i>;define = -DFLEX_SPC
</i><span style="font-style: italic;">i</span><i>ntegrator = md
</i><i>emtol = 100.0
</i><i>emstep = 0.005
</i><i>dt = 0.002 ; ps !
</i><i>nsteps = 25000000 ; total 50 ns
</i><i>nstcomm = 5000
</i><i>nstxout = 5000
</i><i>nstvout = 5000
</i><i>nstfout = 5000
</i><i>nstlog = 5000
</i><i>nstenergy = 5000
</i><i>nstlist = 10
</i><i>ns_type = grid
<br /></i><i>rlist = 1
</i><i>rcoulomb = 1
</i><i>rvdw = 1
</i><i>coulombtype = PME
</i><i>fourierspacing = 0.2
</i><i>pme_order = 6
</i><i>optimize_fft = yes
</i><i>Tcoupl = v-rescale
</i><i>tc-grps = Protein Non-Protein
</i><i>;tau_t = 0.1 0.1
</i><i>tau_t = 0.2 0.2
</i><i>ref_t = 300 300
</i><i>energygrps = A-chain B-chain SOL NA
</i><i>Pcoupl = berendsen
</i><i>Pcoupltype = isotropic
</i><i>;tau_p = 0.1
</i><i>tau_p = 0.25
</i><i>compressibility = 5.4e-5
</i><i>ref_p = 1.0
</i><i>gen_vel = yes
</i><i>gen_temp = 300
</i><i>gen_seed = 173529</i>
<br />
<br />Hsin-Lin
<br /></pre>
</BODY>
</HTML>