On 2013-05-13 21:57, Reza wrote:
So I think I figured out what was causing the discrepancy of Charmm27 energies
between gromacs and NAMD. It appears that it's related to the gromacs version:
energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that
are different from both 4.5.7 and NAMD.
Here are the results form my tests on POPC membrane:
===============================
BOND ANGLE DIH IMP COUL LJ POT
gromacs-4.5.7/gromacs.log
1539.120 3111.902 1250.540 16.284 -1705.306 -1219.345
2993.188
gromacs-4.6.1/gromacs.log
1539.120 3111.902 1250.540 16.284 -5997.992 350.084
269.945
namd-2.9/namd.out
1539.116 3111.920 1250.542 16.284 -1705.307 -1219.343
2993.211
===============================
I think this could be due to either 1) the simulation setup should be different
between 4.5.7 and 4.6.1 when running single point calculations, or 2) my 4.6.1
compilation is not correct (although all regression tests passed), or 3) there
is a bug somewhere.
I'll attach a script that automates the comparison between GROMACS and NAMD in a
separate post (it will make this post > 50kB). If you run it and got
similar/different results as mine, I'll be happy to know. Also any comment on the
simulations setup is highly appreciated.
Reza
Thanks for reporting. I have now created a redmine issue for this
http://redmine.gromacs.org/issues/1249
Could you please upload the datafiles needed to reproduce this there?
Since gmx 4.5.7 is correct we can use that as a reference.
On May 3, 2013, at 11:57 AM, Reza <resa...@gmail.com> wrote:
Actually pdb which is similarly doesn't have velocity information. In this
case however I'm mainly interested to see how the potential terms compare
between the two packages with Charmm27 ff.
Reza
On 5/3/13 11:33 AM, Reza wrote:
Thanks Mark!
No, they weren't. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
You cannot hope to reproduce accurately the energy of a configuration if
you let the coordinates be manipulated.
The "rerun" option is interesting - in my case however the potential energy
terms stayed identical but the kinetic term became zero.
If you are using an .xtc file for the rerun, this makes sense since the .xtc
does not store velocities and hence kinetic energy cannot be calculated.
-Justin
Something you think is equivalent is not :-) Move to testing a system with
two lipids. Inspect all the logfile outputs very carefully for clues.
I totally agree :) So far I found out that for "no cut-off" simulation in
Gromacs, rather that specifying a large cut-off, it needs rlist=rvdw=rcoulomb=0 and
pbc=no along with ns_type=simple and nstlist=0 (according to the manual). I am running
various tests and will update if I find out what is causing the discrepancy.
Reza
On May 1, 2013, at 5:46 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
On Wed, May 1, 2013 at 2:32 PM, Reza Salari <resa...@gmail.com> wrote:
Hi Justin,
I actually did :) but it ended up being bigger than 50 kb so it needed
moderator approval to show up. I was hoping it would've been released by
now. I'll attach a the details below.
Any help/hint is highly appreciated.
Reza
Details:
*1)* Both systems were prepared using VMD "membrane" package and then
waters were removed. I used Gromacs 4.6.1 and NAMD 2.9.
*2)* Simulations were run in vacuum as a single-point energy calculations
(0 step).
No, they weren't. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
You cannot hope to reproduce accurately the energy of a configuration if
you let the coordinates be manipulated.
PME was not used.
*3) *For Gromacs runs, pdb2gmx was used to prepare the system and the
output was saved as the pdb format. The mdp file:
integrator = md
nsteps = 0
nstlog = 1
nstlist = 1
ns_type = grid
rlist = 100.0
coulombtype = cut-off
rcoulomb = 100.0
rvdw = 100.0
pbc = no
*4) *NAMD input file:
structure ../0_prep/memb_nowat.psf
paratypecharmm on
parameters par_all27_prot_lipid.prm
exclude scaled1-4
1-4scaling 1.0
switching off
switchdist 8
cutoff 1000
pairlistdist 1000
margin 0
timestep 1.0
outputenergies 1
outputtiming 1
binaryoutput no
coordinates ../0_prep/memb_nowat.pdb
outputname out
dcdfreq 10
temperature 300
run 0
*5)* Energies:
For Single POPC (kcal/mol)
Gromacs NAMD Diff
Bond 43.0022 43.0015 -0.0007
Angle 80.6568 80.6571 0.0003
Dih 29.8083 29.8083 0.0000
Imp 0.8452 0.8452 0.0000
Coul -17.2983 -17.2983 0.0000
LJ -7.0798 -7.0798 0.0000
Pot 129.9343 129.9340 -0.0003
The intra-molecule terms look fine. Since this is a lipid, there are
non-bonded interactions that are intra-molecule, so the non-bondeds also
seem fine.
For POPC Memb (kcal/mol)
Gromacs NAMD Diff
Bond 1539.1181 1539.1162 -0.0019
Angle 3111.9264 3111.9197 -0.0067
Dih 1250.5425 1250.5421 -0.0004
Imp 16.2837 16.2837 0.0000
Coul -1837.8585 -1705.3075 132.5510
LJ -995.0311 -1219.3432 -224.3121
Pot 3084.9904 2993.2110 -91.7794
Something you think is equivalent is not :-) Move to testing a system with
two lipids. Inspect all the logfile outputs very carefully for clues.
Mark
On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/30/13 4:19 PM, Reza Salari wrote:
Hi
I have set up two small systems, one with a single POPC lipid, and
another
system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
similar comparison as in Table 1 in the Par Bjelkmar et al paper
(porting
charmm ff to gromacs) for my systems. My main question is that for the
single POPC, all the potential energy terms match very well, but for the
membrane system the non-bonding terms differ significantly.
I am providing the full details below and greatly appreciate any hint
for
better comparison of the energies.
Thanks,
Reza Salari
Details:
1) Both systems were prepared using VMD "membrane" package:
2)
It appears you hit "send" too early. Please provide the entirety of the
details you intended. Complete .mdp files and actual quantification of
the
differences you are observing are also very important.
-Justin
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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