[gmx-users] energies in amber, namd and gromacs

Alan alanwilter at gmail.com
Mon Jul 26 16:50:18 CEST 2010

Hi there,

I have a very simple case of a tri alanine (AAA). You can use tleap to
create such peptide and save the pdb and amber's parameters.

Then I do a single point calculation to get the potential energy. I am using
mdin like:

cat << EOF >| mdin
Single point
imin=0, maxcyc=0,

Then I test the same input parameters with Namd2, using namd.conf:

cat << EOF >| AAAamb_namd.conf
outputEnergies 1  # Energy output frequency
DCDfreq        1  # Trajectory file frequency
timestep       2  # in unit of fs
temperature    300  # Initial temp for velocity assignment
cutoff         999
switching      off  # Turn off the switching functions
PME            off  # Use PME for electrostatic calculation
amber          on  # Specify this is AMBER force field
parmfile       AAAamb.prmtop  # Input PARM file
ambercoor      AAAamb.inpcrd  # Input coordinate file
outputname     AAAamb  # Prefix of output files
exclude        scaled1-4
1-4scaling     0.833333  # =1/1.2, default is 1.0
minimize       0

I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the
Elec term, everything else is absolutely the same.

Then comes gromacs. I convert my prmtop and inpcrd to gromcs top and gro
with either acpype or amb2gmx and then doing a single point with file:

cat << EOF >| SPE.mdp
integrator               = md
nsteps                   = 0
dt                       = 0.001
constraints              = none
emtol                    = 10.0
emstep                   = 0.01
nstcomm                  = 1
ns_type                  = simple
nstlist                  = 0
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = no
nstlog = 1
nstenergy = 1
nstvout = 1
nstfout = 1
nstxtcout = 1
comm_mode = ANGULAR

Converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they
don't match amber/namd results. See relative diffs

Bond:    5.87%
Angle:   3.49%
Dihe:    0.14%
vdW:     0.52%
Elec:    0.17%
Pot.Tot: 5.90%

I am very surprised to find this difference, in special for Bond since it's
for this term essentially the same equation and parameters. Any ideas of
what could be missing here?

Many thanks,


Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100726/8b84bc2a/attachment.html>

More information about the gromacs.org_gmx-users mailing list