Dear all,
I experienced the same skipping of frames when concatenating several
trajectories together using trjcat as reported in a thread from 2008
(see below). Apparently the problem has not been resolved. I am using
Gromacs 4.0.7 and each original trajectory was about 200ns long with
frames save
Dear All
I would like to perform MD simulations with benzene as a solvent and
am observing some strange behaviour when I use Lincs to constrain all
the bonds. When I run a fully flexible NPT MD of a box of 320 benzene
molecules simulation at 298K and 1bar, the density comes out at 841
g/l, not to
y
>> solved the problem.
>>
>> I was not sure whether to use nexcl =2 or nexcl =3 in the case of
>> scaled 1-4 interactions, but by trial and error I found that one
>> should use nexcl =3, otherwise you have the full 1-4 interaction + the
>> scaled one, so in total a s
= yes option is not working would be much appreciated.
Thanks to those who responded to my first email,
Mike
On Thu, Jul 2, 2009 at 6:54 PM, Mike Wykes wrote:
> Dear all
>
> I would like to simulate beta cyclodextrin in various organic
> solvents with the OPLSAA FF for Carbohydrat
Dear all
I would like to simulate beta cyclodextrin in various organic
solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18:
1955-1970, 1997) but am having problems with the short range Coulomb
and LJ interactions.
This FF (and OPLS in general) does not assign LJ parameters to
hydrogen
Dear Gromacs Users
I would like to use Gromacs to perform MD on polymers using the OPLSAA
FF. After reading the section of the manual on file formats, I decided
it would be best to create a residue topology file (.rtp) for the
monomer along with a pdb file with the corresponding residue name. Afte
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