Hi,
I have a following issue:
I use the force field CHARMM22-CMAP (that is charmm27-CMAP) in
gromacs to calculate the chignolin.pdb, I want to know the energy items
of just this one conformation. I choose to run a very simple md, just
one step. my input file writes as follows:
md.mdp
emtol = 10
emstep = 0.001
niter = 1
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstcalcenergy = -1
nstenergy = 10
nstxtcout = 100
xtc-precision = 1000
energygrps = System
And I also use CHARMM with the same force field CHARMM22-CMAP, but the
enerCHARMM.pl command to calculate chignolin's energy items. But I found
that their results are quite different. I'd like to list below:
charmm22 gromacs/md22
chignolin(kcal/mol)
angles 20.9848 /
bonds 22.7760 195.141
cmap -0.0595 -0.0684
dihedrals 46.0533 /
elec 19.5690 /
impropers 0.0002 0.014
total 453415.3682 201520.813
ureyb 2.7128 38.779
vdwaals 453303.3316 /
proper dihedral / 46.478
LJ-14 / 82.409
Coulomb-14 / 650.335
LJ (SR) / 201106.699
Coulomb (SR) / -598.990
torsion 45.994 46.4236
= -0.0595 = -0.0684
+ 46.0533 + 46.478
+ 0.0002 + 0.014 ( I
have Unified their unit to kcal/mol)
I want to know why their results shown such a difference? I also use
step=0 and minimization method to try, but nearly the same result.
Theoretically，Two different MD programs calculating one same structure
should give out the results which differ no more than 0.01kcal/mol, but,
this makes me confused. So could you please help me find where the
problem is or the reasons?
Thank you!
Looking forward to your kind reply！
Sincerely yours,
Wei Liu，
w...@itcs.ecnu.edu.cn
East China Normal University
ShangHai，china，200062
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