Thank you Justin for your kind help. The simple reason for considering only
gromos parameter sets is that the parameters for the metal ions (in my
protein) are not defined in other force fields.
On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012376...@n6.nabble.com
On 11/9/13 12:48 AM, pratibha wrote:
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
53A6 is known to under-stabilize helices, so if a helix did not appear in a
simulation using this force field, it is not definitive proof that the structure
does
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012325...@n6.nabble.com wrote:
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
simulations should I consider more
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
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