[gmx-users] trouble minimizing structure with mdrun

Jack Shultz js at drugdiscoveryathome.com
Mon Jan 4 01:38:28 CET 2010

I've been having trouble minimizing a structure using gromacs so I
decided to try using another MD app and see if I can generate a more
relaxed structure.
Using VMD & NAMD I was able to minimize and run MD for this structure
from RCSB.ORG 1YQW.pdb. It was solvated and ionized.

I then took the last frame from a 10,000 step trajectory and exported
it into a pdb file. I preped it so it was compatible with amber99sb
port for gromacs
read it into tleap using amebr99sb and wrote a pdb file from that
Then fixed residues so it it was compatible with gromac

pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh
editconf -bt triclinic -f conf.gro -d 1.0
genbox -cp out.gro -cs ffamber_tip3p.gro
grompp -f em.mdp
echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top
grompp -f em.mdp -c out.gro
mdrun -s topol.tpr -v

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.5 (single precision)
Loaded with Money

Back Off! I just backed up traj.trr to ./#traj.trr.2#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  2.00000e+02
   Number of steps    =        10000
   F-max             =  2.97876e+06 on atom 16106
   F-Norm            =  2.59700e+04

Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106)
Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106)
Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106)


Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298)
Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310)
Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500)
There were 2 inconsistent shifts. Check your topology

em.mdp parameters
define = -DFLEXIBLE
integrator = cg
nsteps = 10000
constraints = none
emtol = 200.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
coulombtype = PME
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes
table-extension = 100
ld_seed = -1



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