<br><br><div class="gmail_quote">On 14 April 2011 02:11, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 14/04/2011 3:40 PM, Moeed wrote:
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">On 13 April 2011 18:45, 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div> On 14/04/2011 10:22 AM, Moeed wrote:
<blockquote type="cite">Hello,<br>
<br>
I have run 2 ns simulations on a hydrocarbon system
(initial density of ~ 2 SI and box size is 15 nm), one
with version 4.0.7 and the other trial using 4.5.3. Both
runs are almost equilibrated to 70 bar pressure but one
is giving density of above 600SI (4.0.7) and the other
density of around 15 SI (4.5.3). With 4.5.3 applying 100
bar pressure does not comrades the system either to the
desired density. I need to study the system at different
pressures from 1 to 70 bar, and I am wondering if the
system can not be compressed with these ref_p values how
can I keep the pressure fixed at P < 70 bar!? <br>
<br>
Please help if you have any idea on why these two
versions are giving inconsistent results and which one
is reliable. <br>
</blockquote>
<br>
</div>
Why are your potential energies positive? What does the
final configuration look like? Why aren't you doing a
"simulated annealing" style of compression with small
increments of delta-P? (These, coincidentally are even good
data for your study...) Massive leaps in ensemble conditions
are often poorly-conditioned for numerical integration.
You're generating velocities that are only approximately
correct, not giving them any chance to equilibrate, and then
smashing the system with massive over-pressure. Small wonder
it might sometimes break...<br>
</div>
</blockquote>
<div><br>
Hi Mark,<br>
<br>
You mean I should get negative potential? I am sure topology
is generated properly. can you explain why this is concerning?<br>
</div>
</div>
</blockquote>
<br></div>
What does a set of charges with positive potential energy want to
do?<div class="im"><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">
<div>
Can you please elaborate on compressing using simulated
annealing? How can I do this?<br>
</div>
</div>
</blockquote>
<br></div>
That's not what I said - I used quotation marks and the word "style"
for a reason. I told you not to do massive changes of conditions,
and to use small increments of delta-P. Equilibrate at one P, change
it a bit. Repeat. This is like simulated annealing, but with P
instead of T.<br></div></blockquote><div><br>Dear Mark,<br><br>I see now what you mean. But actually my problem is not equilibrating..I can follow your advise and equilibrate the system but as I said starting from the same structure and settings, both runs one with 4.0.7 and the other 4.5.3, show that system is pretty close to ref_p = 70 but densities are terrible different. What I dont realize is that how to judge which version is giving correct density. and also version 4.5.3 does not compress with any pressure below 100 bar. So even when I compress using 4.0.7, and try to use output structure from 4.0.7 as input for 4.5.3 to apply say ref_p of 70, my box expands again.<br>
<br>I am stuck on this and it seems the only option is to just stick to version 4.0.7! <br><br>:) <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">
<div>Thanks, :)<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> <br>
When reporting output from .log file and g_energy, please
either use plain text email, or switch to a non-proportional
font like Courier. Those tables make it harder for people to
help you than you want it to be.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite"><br>
4.0.7 <br>
<br>
Statistics over 250001 steps [<b> 1500.0001 thru
2000.0001 ps ],</b> 14 data sets<br>
The term 'Cons. rmsd ()' is averaged over 2501 frames<br>
All other averages are exact over 250001 steps<br>
<br>
Energy Average RMSD
Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Angle 36.9945 0.806738
0.804483 0.0521993 0.208798<br>
Ryckaert-Bell. 9.04227 0.376253
0.371412 0.0521057 0.208424<br>
LJ-14 5.23048 0.119612
0.119611 0.00033983 0.00135933<br>
Coulomb-14 -1.66329 0.104171
0.102175 0.0175753 0.0703015<br>
LJ (SR) -27.3967
0 0 0.0421934 0.168774<br>
Coulomb (SR) 8.98711 0.163579
0.16062 -0.0268199 -0.10728<br>
Potential 31.1944
0 0 0.137594 0.550377<br>
Kinetic En. 51.1009 0.987759
0.987724 0.00725949 0.0290381<br>
Total Energy 82.2953
0 0 0.144851 0.579408<br>
Temperature 299.98 5.79849
5.79828 0.000340897 0.170449<br>
<b>Pressure (bar) 69.3587 414.279
414.256 0.0298385 14.9193</b><br>
Cons. rmsd () 4.01744e-06 1.41883e-07
1.41883e-07 0 0<br>
<b>Box-X 3.04882
0 0 3.57512e-06 0.00178757<br>
Box-Y 3.04882
0 0 3.57512e-</b><br>
<br>
<br>
-----------------------------<br>
4.5.3. <br>
<br>
[<b> 1500.0001 thru 2000.0001 ps ],</b><br>
<br>
Energy Average Err.Est.
RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Angle 37.1357 0.071
0.812307 -0.099711 (kJ/mol)<br>
Ryckaert-Bell. 9.17677 0.14
0.445934 -0.529281 (kJ/mol)<br>
LJ-14 5.18878 0.0087
0.137673 -0.03119 (kJ/mol)<br>
Coulomb-14 -1.60372 0.051
0.126405 -0.144403 (kJ/mol)<br>
LJ (SR) -4.24478 0.29
0.742141 0.697187 (kJ/mol)<br>
Coulomb (SR) 8.97451 0.082
0.198278 0.232025 (kJ/mol)<br>
Potential 54.6272 0.31
1.20733 0.124627 (kJ/mol)<br>
Kinetic En. 51.1047 0.021
0.9945 -0.066306 (kJ/mol)<br>
Total Energy 105.732 0.31
1.58869 0.058321 (kJ/mol)<br>
Temperature 300.002 0.12
5.83806 -0.389239 (K)<br>
<b>Pressure 66.734 5.3
91.83 11.5294 (bar)</b><br>
Constr. rmsd 2.2661e-10 2.3e-10
3.58302e-08 -1.3595e-09 ()<br>
<b>Box-X 11.0055 0.082
0.175309 -0.496198 (nm)<br>
Box-Y 11.0055 0.082
0.175309 -0.496198 (nm)</b><br>
<br>
<br>
<br>
<br>
<br>
<br>
pbc = xyz<br>
<br>
integrator = md <br>
dt = 0.002 <br>
nsteps = 1000000 <br>
nstcomm = 100 <br>
nstenergy = 100 <br>
nstxout = 100 <br>
<br>
nstlist = 10 <br>
ns_type = grid <br>
<br>
coulombtype = Shift<br>
vdw-type = Shift <br>
rcoulomb-switch = 0 <br>
rvdw-switch = 0.9 <br>
rlist = 1.2 <br>
rcoulomb = 1.2 <br>
rvdw = 1.0 <br>
<br>
Tcoupl = v-rescale <br>
tc-grps = System <br>
tau_t = 0.1 <br>
ref_t = 300 <br>
<br>
<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic <br>
tau_p = 1 <br>
compressibility = 4.5e-5 4.5e-5 <br>
ref_p = 70 <br>
<br>
<br>
gen_vel = yes <br>
gen_temp = 300.0 <br>
gen_seed = 173529 <br>
<br>
<br>
constraints = all-bonds <br>
constraint-algorithm = lincs <br>
<br>
</blockquote>
<br>
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</div>
</div>
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