CCL: MD simulation program for saturated enzyme reaction



Hi  kjh950429,
 The quality of MD simulation doesn't depend upon the MD engines such as
 NAMD, Amber, Gromacs etc but it depends upon the force field used. Note
 that  NAMD, AMBER, Hyperchem as you mentioned, are MD engines. You can use
 any of the above programs depending upon its availability for you. In my
 personal opinion (for enzymes), I suggest Amber and Charmm forcefields.
 NAMD is free and it supports both forcefields. Amber MD program (sander) is
 free but as AmberTools. If you want more speedy calculations with amber,
 i.e. pmemd, you have to buy Amber.
 Hope it helps.
 Kshatresh
 On Sat, Dec 1, 2018 at 7:39 PM Kshatresh Dutta Dubey
 <kshatresh---gmail.com>
 wrote:
 > Hi  kjh950429,
 >
 > The MD simulation doesn't depend upon the MD engines such as NAMD, Amber,
 > Gromacs etc but it depends upon the force field used. Note that  NAMD,
 > AMBER, Hyperchem as you mentioned, are MD engines. You can use any of the
 > above programs depending upon its availability for you. In my personal
 > opinion (for enzymes), I suggest Amber and Charmm forcefields. NAMD is free
 > and it supports both forcefields. Amber MD program (sander) is free but as
 > AmberTools. If you want more speedy calculations with amber, i.e. pmemd,
 > you have to buy Amber.
 >
 > Hope it helps.
 > Kshatresh
 >
 > On Sat, Dec 1, 2018 at 7:28 PM kjh950429^_^gmail.com <
 > owner-chemistry---ccl.net> wrote:
 >
 >>
 >> Sent to CCL by: "           " [kjh950429:_:gmail.com]
 >> Hi everyone.
 >> I am currently planning on running a MD simulation for completely
 >> saturated enzymes
 >> (to be more specific, enzymes comprised of about 2,000 or so atoms such
 >> as bovine
 >> liver rhodanese.) I was wondering which program would be best suited to
 >> run the
 >> job: NAMD, AMBER, Hyperchem etc.>>
 >>
 >>
 >
 > --
 > With best regards
 >
 >
 ************************************************************************************************
 > Dr. Kshatresh Dutta Dubey
 > Researcher,
 > Institute of Cell and Molecular Biology
 > Uppsala University
 > Uppsala, Sweden
 >
 >
 >
 --
 With best regards
 ************************************************************************************************
 Dr. Kshatresh Dutta Dubey
 Researcher,
 Institute of Cell and Molecular Biology
 Uppsala University
 Uppsala, Sweden