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

[Reza Salari]

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). 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



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:
>
>> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>