<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">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 text="#000000" bgcolor="#ffffff"><div class="im">
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><br><br>
Can you please elaborate on compressing using simulated annealing? How can I do this?<br><br>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></div><div class="h5"><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>
</div></div></div>
<br>--<br>
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