From wliu at itcs.ecnu.edu.cn Thu Jul 3 15:56:20 2014 From: wliu at itcs.ecnu.edu.cn (wliu) Date: Thu, 03 Jul 2014 13:56:20 -0000 Subject: [Test] =?utf-8?q?why_the_energy_items_in_gromacs_is_different_fro?= =?utf-8?q?m_charmm=3F?= In-Reply-To: References: Message-ID: <0536de5d4a4c84302d3dca0ae4c75c9c@itcs.ecnu.edu.cn> 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? wliu at itcs.ecnu.edu.cn East China Normal University ShangHai?china?200062