[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Reza resal81 at gmail.com
Fri May 3 17:33:19 CEST 2013 

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.

> 
> 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.abraham at gmail.com> wrote:

> On Wed, May 1, 2013 at 2:32 PM, Reza Salari <resal81 at 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 <jalemkul at 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
>>> 
>>> --
>>> ==============================**==========
>>> 
>>> 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<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>> ==============================**==========
>>> --
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