MD wrote:
Hi gromacs experts,
I used gromacs 4.5.3. my system has only spce water, no other types.
In .mdp file,
I used the following parameters;
define =
constraints = none
constraint-algorithm = Lincs
Can u tell me Is it flexible water or all the bond, angle fixed using
the above setting?
Look at spce.itp and/or your md.log file. If the #ifdef FLEXIBLE statement is
not invoked, the SETTLE algorithm is used.
what is the equations of potential energy in Gromacs 4.5 using OPLSAA?
The components of various functional forms are described in the manual.
-Justin
Best regards
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--
========================================
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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