On 2011-11-26 16:38, Igor Druz wrote:
There was no water. Version 4.5.5. Single precision. This is what I ran:
pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.15997e+02 kJ/mol
the pdb has more decimal digits, hence you have two "different" sets of
coordinates.
If you convert the gro back to pdb and the redo the procedure you should
get identical numbers.
The mdp file:
integrator = md
nsteps = 0
nstcomm = 1
nstxout = 1
nstvout = 1
nstfout = 0
nstlog = 1
nstenergy = 1
nstxtcout = 0
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
rcoulomb = 0
rvdw = 0
gen_vel = no
unconstrained-start = yes
lincs-warnangle = 30
The pdb file :
HETATM 1 1HH3 ACE 1 -1.449 0.109 -0.581
H
HETATM 2 CH3 ACE 1 -2.101 -0.268 0.202
C
HETATM 3 2HH3 ACE 1 -1.708 0.090 1.151
H
HETATM 4 3HH3 ACE 1 -2.109 -1.350 0.189
H
HETATM 5 C ACE 1 -3.491 0.269 0.000
C
HETATM 6 O ACE 1 -4.453 -0.401 -0.152
O
ATOM 7 N GLY 2 -3.601 1.734 0.000
N
ATOM 8 H GLY 2 -3.039 2.278 -0.623
H
ATOM 9 CA GLY 2 -4.525 2.391 0.903
C
ATOM 10 HA1 GLY 2 -5.539 2.051 0.696
H
ATOM 11 HA2 GLY 2 -4.263 2.147 1.932
H
ATOM 12 C GLY 2 -4.461 3.901 0.720
C
ATOM 13 O GLY 2 -3.677 4.400 -0.128
O
HETATM 14 N NME 3 -5.316 4.776 1.535
N
HETATM 15 H NME 3 -6.182 4.876 1.044
H
HETATM 16 CH3 NME 3 -4.685 6.072 1.731
C
HETATM 17 1HH3 NME 3 -3.754 5.941 2.272
H
HETATM 18 2HH3 NME 3 -5.328 6.697 2.341
H
HETATM 19 3HH3 NME 3 -4.465 6.615 0.809
H
END
*In reply to chris.neale at utoronto.ca <http://utoronto.ca>:*
It's more useful if you provide more information. What was the .pdb
file (can I download it from the pdb databank?) was there water? what
version of gromacs? was it compiled in double or single precision?
what were your mdp parameters?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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