NAMD GROMACS wrote:
Hi,
Can someone please provide me the link? I couldnt find the link in
gromacs webpage related to these.also in wiki, this is not clearly
described.
A thorough read of Chapter 5 of the manual is probably in order, paying specific
attention to section 5.3.2 and Table 5.4.
-Justin
On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
On Thu, 4 Sep 2008 23:22:35 -0500
"NAMD GROMACS" <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi,
I have a couple of questions regarding top file and forcefield.
1st, in the top file
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 2 ga_9
2 1 4 2 ga_9
2 1 5 2 ga_10
3 1 4 2 ga_9
3 1 5 2 ga_10
Can you please tell me what the word "funct: stands for? what
kind of
functionals, why the numbers 2, and then in case of angles it
changes to 1?
I couldnt find good explanation for this in any manual or tutorial.
there is chapter dedicted to this ... and there the wiki (link at
www.gromacs.org <http://www.gromacs.org/>) ...
Also what does ga_9, ga_10 etc means..I guess the a in ga stands
for angle,
I dont know where the g is coming from. I am guessing the
numbers are
different types of bond.
you should have a look at the paper of the force field.
Question regarding the force-field.
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: [DEPRECATED] Gromacs force field (see manual)
8: [DEPRECATED] Gromacs force field with hydrogens for NMR
9: Encad all-atom force field, using scaled-down vacuum charges
10: Encad all-atom force field, using full solvent charges
Here I am choosing 2 for my peptide in water run. I am wondering
If I need
to study peptide-mineral surface interaction, what number should
I chose? Is
there a way I can go beyond 10, or can I dvelop my own force
field, .top
file for interacting with mineral surface? Any suggestions on
how to develop
new .top file including metals and metal oxide surfaces would be
also great
help.
Thanks
Subhashis
-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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