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

Justin Lemkul jalemkul at vt.edu
Fri May 3 17:44:43 CEST 2013 


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.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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-- 
========================================

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

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