On 2/27/13 10:01 AM, jesmin jahan wrote:
Hi Justin,
Thanks for your reply.
I am able to run it now. I am using the following parameters.
--------------------------------------------------------------------------------------------------------------
constraints = none
integrator = md
cutoff-scheme = Verlet
pbc = xyz
verlet-buffer-drift = -1
dt = 0.001
nsteps = 0
rcoulomb = 1
rvdw = 1
rlist = 1
nstgbradii = 1
rgbradii = 1
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
optimize_fft = yes
energygrps = protein
--------------------------------------------------------------------------------------------
I got the following energy values for this run.
Statistics over 1 steps using 1 frames
Energies (kJ/mol)
GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
-1.52255e+05 5.75419e+08 -2.44085e+05 5.75023e+08 6.36555e+11
Total Energy Temperature Pressure (bar)
6.37130e+11 1.60603e+10 7.90024e+10
###############################################################################
On the other hand, when I used gromacs-4.5.3, with the following parameters:
-----------------------------------------------------------------------------------------------------------------------------------------
constraints = none
integrator = md
pbc = no
dt = 0.001
nsteps = 0
rcoulomb = 300
rvdw = 300
rlist = 300
nstgbradii = 300
rgbradii = 300
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
optimize_fft = yes
energygrps = protein
--------------------------------------------------------------------------------------
I got the following energy values:
Energies (kJ/mol)
GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
-1.58040e+04 0.00000e+00 -2.42022e+05 -2.57826e+05 0.00000e+00
Total Energy Temperature Pressure (bar)
-2.57826e+05 0.00000e+00 0.00000e+00
You can see that there is a huge difference (10 times), in these two
energy values!
How can I get a similar value that I was receiving previously (i.e.,
-1.58040e+04)? The previous energy was correct, while the current
value is 10 times more than the previous one.
Also note that your temperature is about a thousand times hotter than a nuclear
explosion, as well :)
You're comparing dissimilar things in the two setups and expecting them to come
out the same. With 4.6, you're using PBC and explicit cutoffs, in a box that's
likely inappropriate as you have massive atomic overlap (which is what gives
rise to the ridiculous temperature). In the case of 4.5.3 you have a
non-periodic system and thus you can't get overlap between images (because there
are none). Conclusion: your settings for 4.6 simply don't make sense.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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 gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
