Alan wrote:
Thanks dear Chris and Berk.
Indeed I contact Eric but still waiting a reply. BTW, the whole point I
am trying here is to try to reproduce his results and apply to validate
my application ACPYPE, which uses ANTECHAMBER.
Thanks Berk for explaining about the Kinetic energy.
And Chris:
On Tue, Jul 27, 2010 at 15:57, <[email protected]
<mailto:[email protected]>> wrote:
Dear Alan:
(although you should try gromacs compiled in double precision).
I did, same results.
I can reproduce the non-zero kinetic energy with a single spc water,
as long as I add define=-DFLEXIBLE to the .mdp file. The output .gro
contains all zeroes for velocities (as long as the input .gro does not
contain any velocities!):
I was hoping that my error would be something simple like forgetting
"define=-DFLEXIBLE", but adding that made no difference yet.
I added unconstrainted_start=yes to your .mdp file but that did not
help.
I am using GMX 4.0.5 and if I add "unconstrainted_start=yes" I got a error:
WARNING 1 [file SPE.mdp, line unknown]:
Unknown or double left-hand 'unconstrainted_start' in parameter file
I never heard about this option.
Typo: the option "unconstrained_start" should be replaced by "continuation" in
the 4.0.x series; grompp will replace it for you if the old option is present.
-Justin
I tried the same system in CNS/XPLOR and the results matched AMBER and
NAMD. So far only GROMACS looks awkward.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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