[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD
resal81 at gmail.com
Wed May 1 14:32:04 CEST 2013
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.
*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). 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:
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
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
On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/30/13 4:19 PM, Reza Salari wrote:
>> 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.
>> Reza Salari
>> 1) Both systems were prepared using VMD "membrane" package:
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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