[gmx-users] Re: inconsistent energies

[Vlad Isaev]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110108/9296a387/attachment.html>