Thanks, Mark. No, it is not picking any chk files. But the coordinates in the gro file after mdrun change slightly for some of the atoms on using cg and l-bfgs, whereas with steep they remain the same.
e.g., in b4min.gro submitted to cg or l-bfgs or steep: 2GLY O 13 0.736 0.922 -0.350 in min.gro after cg and l-bfgs: 2GLY O 13 0.735 0.920 -0.349 in min.gro after steep: 2GLY O 13 0.736 0.922 -0.350 So, I guess I have to trust steep on this if I just need the energy of the molecule as the coordinates of atoms do not change. By the look of it, AMBER10 also changes coordinates slightly on using: imin=0, maxcyc = 0, ncyc = 0, ntb = 0, cut = 99999 Is there any other way of calculating a single point energy by GROMACS? -Vlad On 8/01/2011 12:10 AM, Vlad Isaev wrote: >* Hi, *>* *>* I want to calculate the energy of a peptide. No minimization, or md, *>* just the energy at 0 K. I use this input: *>* *>* integrator = steep *>* nsteps = 0 *>* nstenergy = 1 *>* nstlist = 0 *>* ns_type = simple *>* pbc = no *>* rlist = 0 *>* rcoulomb = 0 *>* rvdw = 0 *>* *>* *>* I get: *>* *>* Potential Energy = -1.1744482e+02 *>* *>* Changing steep to cg changes the potential energy even though nsteps=0: *>* *>* Potential Energy = -1.2410449e+02 *>* *>* The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion *>* factor 4.184). *>* *>* Any ideas why these are so different? * < That's pretty weird. Please double check that you were really using the < same input coordinates to grompp (and that mdrun wasn't picking up a < checkpoint file). < Mark
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