Dear Justin:
Thank you for your email!
Thanks to your help and explanation, I am feeling more comfortable with
OPLS topology modification.
Before this work, I have used Gromacs without modifying FF paramters for
simulating 'water' in general systems, which can easily obtained from PDB
On Mar 17, 2009, at 8:45 AM, tree wrote:
Dear Justin:
Thank you for your email!
Thanks to your help and explanation, I am feeling more comfortable
with OPLS topology modification.
Before this work, I have used Gromacs without modifying FF paramters
for simulating 'water' in general
Dear Dr. Periole:
Thank you for your answer.
That was the point which I wanted to double check (of course after reading
the manual...).
Thank you again!
Sincerely,
Kim
On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole x.peri...@rug.nl wrote:
On Mar 17, 2009, at 8:45 AM, tree wrote:
Dear
Dear Justin and All:
I truly appreciate your clear answer.
Since my questions are solved by your explanations, I do not know how I
can express my grateful heart.
Now I have to ask second step questions. :)
It is related to the OPLS-aa bon.itp file.
Each section (bonds, angle, diherdal, and
On Mar 16, 2009, at 9:34 AM, tree wrote:
Dear Justin and All:
I truly appreciate your clear answer.
Since my questions are solved by your explanations, I do not know
how I can express my grateful heart.
Now I have to ask second step questions. :)
It is related to the OPLS-aa bon.itp
Dear Dr. Periole:
Thank you for your answer.
You meant that the types of potential functions do not have any relations
with OPLS-aa (except first (1) case).
Those (from 2...) are defined as written the Gromacs manual.
Thank you again.
Sincerely,
Kim
On Mon, Mar 16, 2009 at 5:42 PM, XAvier
Tree wrote:
Dear Dr. Periole:
Thank you for your answer.
You meant that the types of potential functions do not have any
relations with OPLS-aa (except first (1) case).
Those (from 2...) are defined as written the Gromacs manual.
Table 5.4 defines the different types of intramolecular
Dear All:
I appreciate your answer always.
Right now, I am trying to add/modify some values in OPLS-aa FF.
I am confused atom type (opls_xxx) and atom name (e.g., C) in atp,
bon.itp, and nb.itp files.
Please let me try the situation by an example, first.
In atp file,
...
opls_058
Tree wrote:
Dear All:
I appreciate your answer always.
Right now, I am trying to add/modify some values in OPLS-aa FF.
I am confused atom type (opls_xxx) and atom name (e.g., C) in atp,
bon.itp, and nb.itp files.
Please let me try the situation by an example, first.
In atp file,
...
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