[gmx-users] topology file
spoel at xray.bmc.uu.se
Fri Aug 30 19:42:48 CEST 2002
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)
> -----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
> > (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
> > 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.
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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
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