<span style="font-size:10pt;font-family:"Courier New";color:rgb(0,0,0)" lang="PL">grompp -f tpi.mdp
-c tpi.pdb -p topol.top -o tpi.tpr<br><br>where tpi.pdb is a file with extra water molecule as well as topol.top. Then:<br><br></span>
<p class="MsoNormal" style="color:rgb(0,0,0)"><span style="font-size:10pt;font-family:"Courier New"" lang="EN-GB">mdrun –s
tpi.tpr -rerun md.trr -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg</span></p>
<br><span style="font-size:10.0pt;font-family:"Courier New";color:red" lang="PL"><br></span><br><div class="gmail_quote">On Wed, May 9, 2012 at 2:56 PM, Javier Cerezo <span dir="ltr"><<a href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">What's your command line?<br>
<br>
El 09/05/12 15:49, Steven Neumann escribió:<div class="HOEnZb"><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
title = Test Particle Insertion<br>
; Run parameters<br>
integrator = tpi<br>
nsteps = 50000000 ; 100 ns<br>
dt = 0.002 ; 2 fs<br>
; Output control<br>
nstxout = 0 ; suppress .trr output ; output coordinates every 25 ps<br>
nstvout = 25000 ; velocities to output every 25000 steps<br>
nstenergy = 1000 ; save energies every 2 ps<br>
nstlog = 1000 ; update log file every 2 ps<br>
nstxtcout = 100000 ; suppress (tlumic) xtc trajectory<br>
energygrps = System<br>
continuation = no ; first dynamics run<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 cells<br>
nstlist = 5 ; 10 fs<br>
vdwtype = Switch<br>
rvdw-switch = 1.0<br>
rlist = 1.4 ; short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)<br>
ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential rcoulomb<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.12 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc_grps = System ; two coupling groups - more accurate<br>
tau_t = 0.1 ; time constant, in ps<br>
ref_t = 318 ; reference temperature, one for each group, in K<br>
; Pressure coupling is on<br>
pcoupl = Parrinello-Rahman ; pressure coupling is on for 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 = yes ; assign velocities from Maxwell distribution<br>
gen_temp = 318 ; temperature for Maxwell distribution<br>
gen_seed = -1 ; generate a random seed<br>
</blockquote>
<br></div></div><div class="HOEnZb"><div class="h5">
-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
Tel: <a href="tel:%28%2B34%29868887434" value="+34868887434" target="_blank">(+34)868887434</a><br>
-- <br>
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