Did you look at the standard tutorial page? There is a section
specifically for analysis:
http://ambermd.org/tutorials
Also, please start a new thread for a new question rather than tacking it
on the end of an existing thread.
HTH,
Jason
On Wed, Nov 18, 2015 at 4:35 AM, Vishnudatt Pandey <
vishnudattpandey127.gmail.com> wrote:
> Dear sir ,
> I am doing lipid simulation work using lipid force field of
> amber14.I am not getting a idea that how we can analyse our simulation
> result using amber software.please if possible then tell me some related
> link with analysis part and tutorials.
>
> Thanking you
> Vishnudatt Pandey
>
> On Sat, Oct 10, 2015 at 9:56 AM, David A Case <
> dacase.scarletmail.rutgers.edu> wrote:
>
> > On Fri, Oct 09, 2015, Vu Truong wrote:
> > >
> > > Thanks for your response. Yes, I do have nitrogen molecules in my
> system
> > > which is non-standard residues. So do you think if the cut-off distance
> > may
> > > also be the reason for that error?
> >
> > There is no reason, per se, that N2 molecules should cause problems, but
> > double-check the Lennard-Jones and bond parameters you are using. Try a
> > short
> > simulations without the N2 to see if the vlimit messages go away. Look
> for
> > short contacts between the N2 and other atoms in the system.
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 18 2015 - 08:30:05 PST
