[gmx-users] Discrepancy in a single point energy simulation between Gromacs and Namd.
Mark Abraham
mark.j.abraham at gmail.com
Fri Nov 7 18:15:09 CET 2014
Hi,
Best practice for single-points is here
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy, but you
are fortunately avoiding most of the issues by not using constraints.
Last time someone reported a discrepancy like this (AMBER, IIRC) there was
a difference in the way the two codes were shifting the non-bonded
potential to be zero at the cutoff. Your .mdp forces Gromacs to use no
shifts, but I don't know whether you have done so for NAMD, if it is needed
and/or possible. You can try coulomb_modifier = potential-shift.
Mark
On Fri, Nov 7, 2014 at 5:45 PM, IÑIGO SAENZ <inigo.saenz01 at estudiant.upf.edu
> wrote:
> Hi all,
>
> I've got a system of a protein inside a cube of water parametrized with the
> amber ff99SB force-field. I have converted the .prmtop and .pdb files of
> this system into a .gro and .top by means of ACPYPE. The problem is that
> when I perform the single point energy calculation of these system with
> Namd and Gromacs I obtain very opposing results in the Electrostatic energy
> results and I suspect that I'm overlooking some details in the .mdp file
> or in the namd input file. I paste you the results that I obtain with NAMD
> and gromacs and also the configuration files.
>
>
> BOND: 38088.4829 38081.7399
> ANGLE: 1573.6867 1573.7189
> DIHEDRAL: 9873.2782 9872.7127
> COULOMB: -179655.6187 141241 (1-4 interactions) -1.84836e+07 (short
> range)
> VDW: 21796.8418 21797.2514
>
> First column corresponds to NAMD results and the second one to Gromacs
> results,
> Now, the *SPE.mdp file*
>
> define = -DFLEXIBLE
> integrator = md
> nsteps = 0
> dt = 0.001
> constraints = none
> nstcomm = 1
> ns_type = simple
> nstlist = 1
> coulombtype = cut-off
> vdw_modifier = none
> coulomb_modifier = none
> rlist = 0.9
> rcoulomb = 0.9
> rvdw = 0.9
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 1
> pbc = xyz
> nstlog = 1
> nstenergy = 1
> nstvout = 1
> nstfout = 1
> nstxtcout = 1
> comm_mode = ANGULAR
> continuation = yes
>
> *NAMD.conf file:*
>
> rigidBonds none
> timestep 2
> temperature 0
> cutoff 9
> switching off
> PME off
> cellBasisVector1 117.210 0 0
> cellBasisVector2 0 94.119 0
> cellBasisVector3 0 0 78.923
> # NAMD doesn't force neutralisation of charge
> amber on # Specify this is AMBER force field
> parmfile parameters # Input PARM file
> ambercoor s.inpcrd # Input coordinate file
> outputname run_namd # Prefix of output files
> exclude scaled1-4
> 1-4scaling 0.8333 # =1/1.2, default is 1.0
> run 0 ;# 2ps
>
> I should mention that in .gro I put the box size correctly, the same values
> that the box-size values that appear in the NAMD.conf file divided by 10 to
> convert them to nanometers.
>
> I'm desperate with this error, please, any help would be highly
> appreciated! If you need more information about this problem, feel free to
> ask me.
>
> Thank you very much in advance!
> --
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