[gmx-users] CHARMM36 GROMACS implementation

[John Whittaker]

Hi Justin, thanks for the reply and the good idea.

I checked a configuration of my system using both force fields and, for
the information of anyone who may have a similar problem in the future,
found using gmx energy:

CHARMM36 from Tom Piggot on GROMACS website:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
---------------------------------------------------------------------------
Bond                         8026.4         --          0          0
LJ-14                       3825.57         --          0          0
Coulomb-14                 -66212.1         --          0          0
LJ (SR)                    -6600.53         --          0          0
Coulomb (SR)                -238906         --          0          0
Potential                   -223757         --          0          0
Kinetic En.                  101836         --          0          0
Total Energy                -121921         --          0          0

CHARMM36 official implementation from MacKerell lab website:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
---------------------------------------------------------------------------
Bond                         8026.4         --          0          0
LJ-14                       3825.56         --          0          0
Coulomb-14                 -66212.1         --          0          0
LJ (SR)                    -6600.04         --          0          0
Coulomb (SR)                -238906         --          0          0
Potential                   -223757         --          0          0
Kinetic En.                  101836         --          0          0
Total Energy                -121921         --          0          0

So, from the PE/KE/E-total values, the force fields are equivalent for my
system of DPPC and CHARMM-TIP3P. But curiously, I noticed the LJ values
are slightly different for each (LJ-14, 3825.57/3825.56) and (LJ (SR),
-6600.53/-6600.04). Should I concern myself at all with this difference?
Both single-point reruns were processed and ran using 5.1.2.

Out of curiosity, I also grompp'd and reran using 5.1.5. This time I
received the exact same LJ-14 and LJ (SR) values as in 5.1.2 (but still
those small differences between the force field) but the overall values of
the potential energy for both force fields was different than in 5.1.2 (by
14 kJ/mol).

Is there a simple explanation for why this might happen?

Thanks again in advance for any help.

John

>
>
> On 11/19/18 11:32 AM, John Whittaker wrote:
>> Hi all,
>>
>> I am trying to reproduce the pure DPPC bilayer data found in J. Chem.
>> Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935)
>> using
>> the recommended protocol given in the paper.
>>
>> Recently, I realized I made a mistake and have been using the CHARMM36
>> forcefield provided by Tom Piggot here
>> (http://www.gromacs.org/Downloads_of_outdated_releases/User_contributions/Force_fields)
>> rather than the official CHARMM36 implementation found on the MacKerell
>> lab's site (http://mackerell.umaryland.edu/charmm_ff.shtml).
>>
>>  From what I understand from its description in the force field
>> documentation and the accompanying paper, the version provided by Tom
>> Piggot should not affect my results because the lipid parameters from
>> CHARMM36 are unchanged (while the protein parameters are) and my system
>> consists only of water and DPPC.
>>
>> Am I right to assume that my results should be (theoretically)
>> reflective
>> of those that I would obtain from using the using the full CHARMM36
>> force
>> field?
>
> The lipids should all be the same. A single-point energy/force
> evaluation under both force fields would confirm this.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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>
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