Moeed wrote:
On 14 April 2011 02:11, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 14/04/2011 3:40 PM, Moeed wrote:
On 13 April 2011 18:45, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
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!?
Please help if you have any idea on why these two versions
are giving inconsistent results and which one is reliable.
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...
Hi Mark,
You mean I should get negative potential? I am sure topology is
generated properly. can you explain why this is concerning?
What does a set of charges with positive potential energy want to do?
Can you please elaborate on compressing using simulated annealing?
How can I do this?
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.
Dear Mark,
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.
I am stuck on this and it seems the only option is to just stick to
version 4.0.7!
Upgrade to version 4.5.4. There was a bug involving the output of
pressure-related terms that was fixed. This may or may not be relevant, but
before making such conclusions, always verify your conclusions with the latest
bugfix release.
-Justin
:)
Mark
Thanks, :)
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.
Mark
4.0.7
Statistics over 250001 steps [* 1500.0001 thru 2000.0001 ps
],* 14 data sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps
Energy Average RMSD
Fluct. Drift Tot-Drift
-------------------------------------------------------------------------------
Angle 36.9945 0.806738 0.804483
0.0521993 0.208798
Ryckaert-Bell. 9.04227 0.376253 0.371412
0.0521057 0.208424
LJ-14 5.23048 0.119612 0.119611
0.00033983 0.00135933
Coulomb-14 -1.66329 0.104171 0.102175
0.0175753 0.0703015
LJ (SR) -27.3967 0 0
0.0421934 0.168774
Coulomb (SR) 8.98711 0.163579 0.16062
-0.0268199 -0.10728
Potential 31.1944 0 0
0.137594 0.550377
Kinetic En. 51.1009 0.987759 0.987724
0.00725949 0.0290381
Total Energy 82.2953 0 0
0.144851 0.579408
Temperature 299.98 5.79849 5.79828
0.000340897 0.170449
*Pressure (bar) 69.3587 414.279 414.256
0.0298385 14.9193*
Cons. rmsd () 4.01744e-06 1.41883e-07
1.41883e-07 0 0
*Box-X 3.04882 0 0
3.57512e-06 0.00178757
Box-Y 3.04882 0 0
3.57512e-*
-----------------------------
4.5.3.
[* 1500.0001 thru 2000.0001 ps ],*
Energy Average Err.Est. RMSD
Tot-Drift
-------------------------------------------------------------------------------
Angle 37.1357 0.071 0.812307
-0.099711 (kJ/mol)
Ryckaert-Bell. 9.17677 0.14 0.445934
-0.529281 (kJ/mol)
LJ-14 5.18878 0.0087 0.137673
-0.03119 (kJ/mol)
Coulomb-14 -1.60372 0.051 0.126405
-0.144403 (kJ/mol)
LJ (SR) -4.24478 0.29 0.742141
0.697187 (kJ/mol)
Coulomb (SR) 8.97451 0.082 0.198278
0.232025 (kJ/mol)
Potential 54.6272 0.31 1.20733
0.124627 (kJ/mol)
Kinetic En. 51.1047 0.021 0.9945
-0.066306 (kJ/mol)
Total Energy 105.732 0.31 1.58869
0.058321 (kJ/mol)
Temperature 300.002 0.12 5.83806
-0.389239 (K)
*Pressure 66.734 5.3 91.83
11.5294 (bar)*
Constr. rmsd 2.2661e-10 2.3e-10 3.58302e-08
-1.3595e-09 ()
*Box-X 11.0055 0.082 0.175309
-0.496198 (nm)
Box-Y 11.0055 0.082 0.175309
-0.496198 (nm)*
pbc = xyz
integrator = md
dt = 0.002
nsteps = 1000000
nstcomm = 100
nstenergy = 100
nstxout = 100
nstlist = 10
ns_type = grid
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.0
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1
compressibility = 4.5e-5 4.5e-5
ref_p = 70
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = lincs
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
