There is no need to post twice, I saw your first post. Your level of questions
indicates that you still do not understand the topology file format. It is
essential that you understand exactly how it works and what is going on or else
you are more likely to have errors in your simulation. I am happy to get you
started, but when you encounter your next problem (probably regarding correct
treatment of opls water oxygen?) you will be able to solve it yourself if you
have taken the time to understand how this works.
1) Your [ atomtypes ] section should have:
H H 1 1.00800 0.400 A 0.00000e+00 0.00000e+00 ;
opls_369
But then you can ignore H in other sections since the LJ is actually zero.
###
2) copy the entire pairs section and paste it under itself:
original:
[pairs]
1 2
1 3
double:
1 2
1 3
1 2
1 3
###
Chris.
-- original message --
Hi all,
Two days back I posted this question, no one replied thats why I am posting
again.
I wanted to use OPLS-AA/L force field for POPC and Protein
1.I calculated the sigma and epsilon values as the way Mr.Justin mentioned
, the values I got are
;name name charge mass charge ptype sigma epsilon
LO LO 1 15.9994 0.000 A 0.295999914
0.878694594 ;carbonyl O, OPLS
LOM LOM 1 15.9994 0.000 A 0.295999914
0.878694594 ;carboxyl O, OPLS
LNL LNL 1 14.0067 0.000 A 3.35300e-03
3.95100e-06 ;Nitrogen, OPLS
2. Then in first step of Chris procedure(web link quoted below), wrote that
add atom type H from opls_369 to match H expected by pope.itp
http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
In archives H atom type adding problem posted for pope type of lipids
opls_369 H 1 1.008 0.400 A 0.0000e+00 0.0000e+00 (for
pope)
Im using POPC type of lipid
I want to ask two things
1. How can I modify H atom type in popc.itp file
2. Mr. Chris mentioned that Parameters require a double pairs section, how
can I mention?
Pls give me detail explanation, Eagerly waiting for reply
all comments will be appreciated
Thanks in advance
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