Hi There,<br><br>I want to use a large simulation box. I did a trial
with 15 * 15 * 15 nm box for 100 steps. genbox_d generates 110k water
molecules, or 330k atoms.<br><br>It looks like that gromacs can run that
large number of atoms. I am sure it will take a long long long time.
However if I really want to simulate it, is there any way that I can
increase the speed? (except using a better cpu, or paralleling it)
Thanks.<br>
<br>My second question is that: If I have to use clusters or super
computer, which one is better? and, do I need a particular
software/program to paralleling it? Thanks.<br><br>Thank you for your
comments and help!<br>Yan<br>
<br>I put my .mdp below:<br>integrator = md<br>dt
= 0.002<br>; duration 2000 ps<br>nsteps = 100<br>comm_mode
= linear<br>nstcomm = 1<br>; dump config every 300 fs<br>
nstxout = 10<br>nstvout = 10<br>nstfout
= 10<br>nstcheckpoint = 100<br>nstlog
= 10<br>nstenergy = 10<br>nstxtcout = 10<br>
xtc-precision = 1000000<br>nstlist = 1<br>ns_type
= grid<br>pbc = xyz<br>rlist =
1.0 ;1.0<br>coulombtype = PME<br>rcoulomb
= 1.0 ;1.0<br>
fourierspacing = 0.2 ;0.1<br>pme_order = 4<br>ewald_rtol
= 1e-5<br>optimize_fft = yes<br>vdwtype =
cut-off<br>rvdw = 1.0 ;1.0<br>tcoupl
= Nose-Hoover<br>
tc_grps = system <br>tau_t = 0.5 <br>ref_t
= 300.0<br>Pcoupl = no<br>annealing = no <br>gen_vel
= no <br>gen_temp = 300.0<br>
gen_seed = 173529<br>constraints = none<br>;energy_excl
= C_H C_H<br>constraint_algorithm = lincs<br>unconstrained_start
= no<br>lincs_order = 4<br>lincs_iter = 1