Hi, <br><br>Thank everyone for your suggestions. <br><br>I have tried to put less molecule in a small box and find this works! Eventually I have solve the problem by using a larger initial box size for the random generated position and orientation. It seemed that the overall interaction of OPLS-AA between ethanes is attractive rather than repulsive, which leads to atomic clashes...<br>
<br>The original box size was calculated from experimental density but apparently this does not work for the OPLS-AA. I had used larger initial box size previously (20% larger than experimental calculated box size) but it did not work out and then I gave up on this direction. Now, I have tried to enlarge the box size by 40% and everything works!<br>
<br>Finally I should offer my gratitude to all of you. Thank you!<br><br>Best,<br>Phil<br><br><div class="gmail_quote">On Tue, Sep 6, 2011 at 10:59 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div>
On 7/09/2011 12:40 AM, Phil (Yang) Song wrote:
<blockquote type="cite">
<div class="gmail_quote">
<div>
<div>
<div class="gmail_quote">Hi, all<br>
<div class="gmail_quote"><br>
I am learning GROMACS 4.5.1 recently and encountered a
problem that puzzled me for weeks. I am wondering if
someone can help me with this.<br>
<br>
Here is the problem: I was trying to perform a MD
simulation for 216 ethane molecules in a box. I have
first generated a box of ethane with random position and
orientation.</div>
</div>
</div>
</div>
</div>
</blockquote>
<br></div>
That's almost certainly inappropriate. Atomic clashes are
inevitable, and EM will not fix severe problems.<br>
<br>
Get a single molecule in a small box, and use genconf to replicate
it. Then use EM and equilibrate thoroughly to remove the residual
ordering. Judicious use of NPT will fix your density to whatever you
want.<br><font color="#888888">
<br>
Mark</font><div><div></div><div><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">
<div>
<div>
<div class="gmail_quote">
<div class="gmail_quote"> Then, I wanted to run a
minimization for the box of ethane to get rid of close
contact of the randomly ethane molecules. However, I
have found that some of the <span>ethane</span>
molecules laid on top of each other after minimization
and infinity forces were resulted. <br>
<br>
Since my mdp file was successfully used to generate
other type of molecules such as acetylene and ethylene
and they should be correct. Also, I have tried to use
conjugate gradient instead of steepest decent for the
minimization, but this effort came out to be in vain. <br>
<br>
Later, I thought the topology file should be the source
of error. I have carefully checked the topology file for
couple of times but did not find any obvious error. I
have also tried to change the charges on each atom in
the ethane to 0 and then run the minimization. Again,
the ethane was attracted into each other. Hence, I think
the vdw could be the problem. However, the parameters of
the vdw interaction are all from the opls-aa files that
come with gromacs and it should be fine.<br>
<br>
Eventually, I am puzzled... <br>
<br>
I am iterating the content of the content of mdp input
file and itp file in the email and also attaching the
input and output of my result as a tarball. Hope someone
can help me to solve this problem.<br>
<br>
Thank you in advance!<br>
<br>
Best,<br>
Phil Song<br>
<font color="#888888"><br>
================================================================================<br>
MDP file<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; preprocessing options<br>
<br>
; title of the simulation<br>
title =<br>
<br>
; include path<br>
include =<br>
<br>
; cpp flag<br>
define =<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; energy minimization<br>
integrator = steep<br>
<br>
; Start time and timestep in ps<br>
tinit = 0<br>
dt = 0.001<br>
nsteps = 500<br>
<br>
; run continuation or reperforming<br>
init_step = 0<br>
<br>
emtol = 1000.0<br>
emstep = 0.01<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; periodic boundary conditions<br>
pbc = xyz<br>
<br>
periodic_molecules = no<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; electrostatics and vdw options<br>
; electrostatics method<br>
coulombtype = PME<br>
rcoulomb = 1.3<br>
<br>
; fourier setup for PME<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
<br>
ewald_geometry = 3d<br>
<br>
; vdw cutoff<br>
rvdw-switch = 0<br>
rvdw = 1.31<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; neighbor list options<br>
; neighbor list frequency<br>
nstlist = 10<br>
<br>
; neighbor search algorithm <br>
ns_type = grid<br>
<br>
; neighbor list cut-off<br>
rlist = 1.30<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; thermostat and barostat<br>
tcoupl = v-rescale<br>
tc_grps = System<br>
ref_t = 50.5<br>
tau_t = 0.5<br>
<br>
pcoupl = berendsen<br>
pcoupltype = isotropic<br>
nstpcouple = 10<br>
ref_p = 1.01325<br>
tau_p = 1.0<br>
<br>
; Using compressibility of ethanol at 273.1
(approximately)<br>
; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164<br>
<br>
compressibility = 1.0e-5<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; velocty generation<br>
gen_vel = yes<br>
gen_temp = 50.5<br>
; gen_seed = 173529<br>
<br>
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; output control options<br>
; output frequency for coords, velocities and forces<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstfout = 5000<br>
<br>
; output frequency for energy<br>
nstenergy = 5000<br>
; energygrps =<br>
<br>
; output frequency for log<br>
nstlog = 5000<br>
<br>
; output options for trajectory<br>
nstxtcout = 5000<br>
xtc_precision = 100000<br>
; xtc_grps =<br>
</font><br>
<font color="#888888"><br>
================================================================================<br>
ITP file<br>
<br>
; Ethane:<br>
; Assign of the atom index<br>
;<br>
; H2 H6<br>
; | | <br>
; H3 - C1 - C5 - H7<br>
; | | <br>
; H4 H8<br>
;<br>
<br>
[ moleculetype ]<br>
; name nrexcl<br>
Ethane 3<br>
<br>
[ atoms ]<br>
; nr type resnr residu atom cgnr
charge mass<br>
1 opls_135 1 ETH CE1
1 -0.18 <br>
2 opls_140 1 ETH HE2
1 0.06 <br>
3 opls_140 1 ETH HE3
1 0.06 <br>
4 opls_140 1 ETH HE4
1 0.06 <br>
5 opls_135 1 ETH CE5
2 -0.18<br>
6 opls_140 1 ETH HE6
2 0.06<br>
7 opls_140 1 ETH HE7
2 0.06 <br>
8 opls_140 1 ETH HE8
2 0.06<br>
<br>
[ bonds ]<br>
; ai aj funct c0 c1<br>
1 5 1<br>
2 1 1<br>
3 1 1<br>
4 1 1<br>
6 5 1<br>
7 5 1<br>
8 5 1<br>
<br>
[ pairs ]<br>
; ai aj funct<br>
2 6<br>
2 7<br>
2 8<br>
3 6<br>
3 7<br>
3 8<br>
4 6<br>
4 7<br>
4 8<br>
<br>
[ angles ]<br>
; ai aj ak funct c0 c1<br>
; H3-C-C<br>
2 1 5 1<br>
3 1 5 1<br>
4 1 5 1<br>
; H-C-H<br>
2 1 3 1<br>
2 1 4 1<br>
3 1 4 1<br>
; C-C-H3<br>
6 5 1 1<br>
7 5 1 1<br>
8 5 1 1<br>
; H-C-H<br>
6 5 7 1<br>
6 5 8 1<br>
7 5 8 1<br>
<br>
[ dihedrals ]<br>
; ai aj ak al funct c0
c1 c2 c3 c4 <br>
2 1 5 6 3<br>
3 1 5 6 3<br>
4 1 5 6 3<br>
2 1 5 7 3<br>
3 1 5 7 3<br>
4 1 5 7 3<br>
2 1 5 8 3<br>
3 1 5 8 3<br>
4 1 5 8 3<br>
<br>
<br clear="all">
</font></div>
<font color="#888888"><br>
-- <br>
Phil (Yang) Song<br>
Room 509, 590 Comm. Ave.<br>
Chem. Dept., Boston Univ.<br>
Boston, MA, 02215, USA</font><br>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Chem. Dept., Boston Univ.<br>Boston, MA, 02215, USA<br><br>