[gmx-users] Re: 1-4 scaling problem?

[chris.neale at utoronto.ca]

Dear Anindita,

There is good reason to keep this on the mailing list.

I am happy to help, but you are misrepresenting the situation
to say that you received no answer on the mailing list. In fact,
you received quite a bit of assistance:

http://www.gromacs.org/pipermail/gmx-users/2008-May/034064.html
http://www.gromacs.org/pipermail/gmx-users/2008-May/034059.html
http://www.gromacs.org/pipermail/gmx-users/2008-May/034062.html (my own reply)
http://www.gromacs.org/pipermail/gmx-users/2008-May/034070.html (my own reply)
http://www.gromacs.org/pipermail/gmx-users/2008-May/034123.html
http://www.gromacs.org/pipermail/gmx-users/2008-May/033999.html

I have seen some of your latest posts on the mailing list, but since you
did not take any action since I asked you to post in simple text to  
the mailing
list, I started ignoring your posts. The &nsbp fields make it impossible for
me to read your posts without a huge amount of work. Look into your email
client ant set it to simple text formatting (i.e. turn off your html  
formatting
on your emails)!

 From a quick look:

1) Your [pairs] are highly non-standard. Why are you commenting out
some of them? e.g.
;      1       6       1
;      2       6       1

2) You appear to have changed your .mdp as per suggestions on the  
list, but please tell us about that since it saves us investigative  
work to know that
you have addressed some specific concerns.

3) Your LO LO [ pairtypes ] looks correct. I did not check the others.

Please post the files that you attached to the email that you sent me  
in some way that others can see them and possibly help you. Also  
please ensure that you overcome your &nsbp problem when you post those  
to the list. I remain unwilling to wade through the hundreds of &nsbp  
fields.

A question: what are the experimental values for DMPC at 300K? I did  
not work directly with DMPC before. I use POPC at 323K mostly, and  
sometimes I use POPC at 310K.

I am going away for the weekend. Once you have posted the relevant  
information to the list and solved your &nsbp problems, then I will  
take a deeper look into the problems that you are experiencing.

Chris.




Quoting ANINDITA GAYEN <aninditagayen at yahoo.co.in>:

>
> dear sir,
>
>
>
> &nbsp; I am facing a dmpc bilayer area (the dmpc_npat.pdb and dmpc.itp
> and lipid.itp from Tieleman's site) problem the origin of which is
> the mistake in 1-4 scaling i think. I have gone through your
> instructuctions about the half-epsilon double pairlist method to
> combine berger-opls, but i think i myself have done something wrong
> executing it.
>
>
>
> my ffoplsmd.itp looks like
>
>
>
>
>
>
>
>
>
>
>
>
>
> #define _FF_OPLS
> #define _FF_OPLSAA
>
> ; This force field uses a format that requires Gromacs 3.1.4 or later.
> ;
> ; References for the OPLS-AA force field:
> ;
> ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
> ; J. Am. Chem. Soc. 118, 11225-11236 (1996).
> ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
> ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
> ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
> ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
> ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001)..
> ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen,   
> J. Phys.. Chem. B 105, 6474 (2001).
> ;
>
> [ defaults ]
> ; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
> 1		3		yes		0.5	0.5
>
> #include "ffoplsaanbmd.itp"
> #include "ffoplsaabon.itp"
>
> The ffoplsaanbmd.itp and dmpcopls14.itp are attached here.
>
> the problem is the bilayer area is shrinking from 59A2 to 55A2 in   
> 500ps run only.
>
> I am sorry for mailing you personally but I have mailed in gmx-users  
>  for several times before, and received no answer.
>
> My md.mdp file is also attached.
>
>
> Please, help me, is my topology files correctly scaled?
>
> Awaiting reply,
>
>
> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
> Sincerely yours,
> Ms. Anindita Gayen
>
> C/O Dr. Chaitali Mukhopadhyay
> Senior Research Fellow
>
> Department of Chemistry
>
> University of Calcutta
>
> 92, A. P. C. Road
>
> Kolkata-700 009
>
> India
>
>
>       BMR - a key player in weight issues. Know more -   
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