[gmx-users] topology file

[David]

On Fri, 2002-08-30 at 18:32, Shrivastava, Indira (NCI) wrote:
>  
>  Hi Gromacs_users, 
>  
>  Can some of the 'topology builders' tell me what 'cp' and 'mult' stands
>  for in the topology file, under the dihedrals?? 
cp = force constant
mult = multiplicity (n in the equation in the manual)
> 
>  Thanks, 
>  Indira 
> 
> -----Original Message-----
> From: Erik Lindahl [mailto:lindahl at stanford.edu]
> Sent: Thursday, August 22, 2002 1:23 PM
> To: Shrivastava, Indira (NCI)
> Cc: 'gmx-users at gromacs.org'
> Subject: Re: [gmx-users] topology file
> 
> 
> Shrivastava, Indira (NCI) wrote:
> >  Hi All, 
> > 
> >  I would like to make a 'top' file for a lysolipid
> (lysophosphatidylcholine
> > (L-POPC))
> >  This lipid is a single chain lipid, with the same headgroup as
> > phosphatidylcholine (POPC).
> >  Can I use the forcefield parameters of POPC to create a top file for
> > (L-POPC) since they
> >  are essentially identical, the only difference being in POPC there are
> two
> > chains whereas in 
> > L-POPC there is only one chain. 
> > 
> 
> Yes, that's what I would do. Lipid topologies are quite easy to edit 
> manually even if it might seem hard the first couple of times.
> 
> If possible, keep the headgroup and the first chain to avoid renumbering 
> any atoms, and then edit the remaining bonds/angles/dihedrals if you 
> need to.
> 
> To test things, run a short simulation of a single lipid in vacuum and 
> check it with ngmx. Since ngmx shows the real bonds defined in the tpr 
> file (in contrast to e.g. rasmol which draws a bond whenever two atoms 
> are close) you can see if the connectivity is correct. You also want to
> make sure that the energies for angles and dihedrals are reasonable
> for the corresponding number of degrees of freedom.
> 
> Cheers,
> 
> Erik
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++